Gap Filling of 3-D Microvascular Networks by Tensor Voting

We present a new algorithm which merges discontinuities in 3-D images of tubular structures presenting undesirable gaps. The application of the proposed method is mainly associated to large 3-D images of microvascular networks. In order to recover the real network topology, we need to fill the gaps between the closest discontinuous vessels. The algorithm presented in this paper aims at achieving this goal. This algorithm is based on the skeletonization of the segmented network followed by a tensor voting method. It permits to merge the most common kinds of discontinuities found in microvascular networks. It is robust, easy to use, and relatively fast. The microvascular network images were obtained using synchrotron tomography imaging at the European Synchrotron Radiation Facility. These images exhibit samples of intracortical networks. Representative results are illustrated

Coupling and robustness of intra-cortical vascular territories

Vascular domains have been described as being coupled to neuronal functional units enabling dynamic blood supply to the cerebral cyto-architecture. Recent experiments have shown that penetrating arterioles of the grey matter are the building blocks for such units. Nevertheless, vascular territories are still poorly known, as the collection and analysis of large three-dimensional micro-vascular networks are difficult. By using an exhaustive reconstruction of the micro-vascular network in an 18 mm 3 volume of marmoset cerebral cortex, we numerically computed the blood flow in each blood vessel. We thus defined arterial and venular territories and examined their overlap. A large part of the intracortical vascular network was found to be supplied by several arteries and drained by several venules. We quantified this multiple potential to compensate for deficiencies by introducing a new robustness parameter. Robustness proved to be positively correlated with cortical depth and a systematic investigation of coupling maps indicated local patterns of overlap between neighbouring arteries and neighbouring venules. However, arterio-venular coupling did not have a spatial pattern of overlap but showed locally preferential functional coupling, especially of one artery with two venules, supporting the notion of vascular units. We concluded that intra-cortical perfusion in the primate was characterised by both very narrow functional beds and a large capacity for compensatory redistribution, far beyond the nearest neighbour collaterals

Spatially Adaptive Mixture Modeling for Analysis of fMRI Time Series.

International audienceWithin-subject analysis in fMRI essentially addresses two problems, the detection of brain regions eliciting evoked activity and the estimation of the underlying dynamics. In [1, 2], a detection-estimation framework has been proposed to tackle these problems jointly, since they are connected to one another. In the Bayesian formalism, detection is achieved by modeling activating and non-activating voxels through independent mixture models (IMM) within each region while hemodynamic response estimation is performed at a regional scale in a nonparametric way. Instead of IMMs, in this paper we take advantage of spatial mixture models (SMM) for their non-linear spatial regularizing properties. The proposed method is unsupervised and spatially adaptive in the sense that the amount of spatial correlation is automatically tuned from the data and this setting automatically varies across brain regions. In addition, the level of regularization is specific to each experimental condition since both the signal-to-noise ratio and the activation pattern may vary across stimulus types in a given brain region. These aspects require the precise estimation of multiple partition functions of underlying Ising fields. This is addressed efficiently using first path sampling for a small subset of fields and then using a recently developed fast extrapolation technique for the large remaining set. Simulation results emphasize that detection relying on supervised SMM outperforms its IMM counterpart and that unsupervised spatial mixture models achieve similar results without any hand-tuning of the correlation parameter. On real datasets, the gain is illustrated in a localizer fMRI experiment: brain activations appear more spatially resolved using SMM in comparison with classical General Linear Model (GLM)-based approaches, while estimating a specific parcel-based HRF shape. Our approach therefore validates the treatment of unsmoothed fMRI data without fixed GLM definition at the subject level and makes also the classical strategy of spatial Gaussian filtering deprecated

How to calculate the barycenter of a weighted graph

Discrete structures like graphs make it possible to naturally and exibly model complex phenomena. Since graphs that represent various types of information are increasingly available today, their analysis has become a popular subject of research. The graphs studied in the field of data science at this time generally have a large number of nodes that are not fairly weighted and connected to each other, translating a structural specification of the data. Yet, even an algorithm for locating the average position in graphs is lacking although this knowledge would be of primary interest for statistical or representation problems. In this work, we develop a stochastic algorithm for finding the Fréchet mean of weighted undirected metric graphs. This method relies on a noisy simulated annealing algorithm dealt with using homogenization. We then illustrate our algorithm with two examples (subgraphs of a social network and of a collaboration and citation network)

Effects of phenology and the microclimate on the seed set of Anemone nemorosa

Changing climate affects the dispersal and phenology of plants and pollinators. Particularly in the spring, climate warming accelerates the timing of flowering and insect emergence. Temporal mismatch is a fairly well studied biological phenomenon. Nevertheless the phenomenon has been studied only for a small number of systems and organisms, and more empirical evidence to show that mismatch occurs and how it is affected by changes in environment. The lack of studies that directly address the effects of this type of phenological mismatches on plant seed set makes it difficult to predict how plant reproductive output will be affected. Although it is reasonable to assume that the reduced seed set is a general response. This response varies greatly among species, which highlights the need for better empirical data. In current the study, the aim is to investigate how the microclimate and flowering time can have an impact on the seed set. The effect of the pollinator on the seed production in a wild flower (Anemone nemorosa) was measured at two different flowering times. Three treatments (a) self-pollination (b) hand-pollination and (c) wild-pollination, were applied during both flowering times: one in mid of April (early spring) and the other in early May (late spring). Pollinator abundance was measured at all the experimental sites and the seed sets were counted in collected flowers. The results show that the flowering time has significantly affected the fertile seed production. However microclimate did not had significant effect fertile seed production. Moreover, during the both flowering times, the variation in the abundance and diversity of the pollinator were not detected, thus the microclimate has an effect on the abundance and diversity of pollinator. There was no significant relationship between the pollinator diversity, abundance and seed set. In conclusion, flowering significantly affects the production of seed set in Anemone nemorosa

Mixture of Kernels and Iterated Semidirect Product of Diffeomorphisms Groups

In the framework of large deformation diffeomorphic metric mapping (LDDMM), we develop a multi-scale theory for the diffeomorphism group based on previous works. The purpose of the paper is (1) to develop in details a variational approach for multi-scale analysis of diffeomorphisms, (2) to generalise to several scales the semidirect product representation and (3) to illustrate the resulting diffeomorphic decomposition on synthetic and real images. We also show that the approaches presented in other papers and the mixture of kernels are equivalent.Comment: 21 pages, revised version without section on evaluatio

How to calculate the barycenter of a weighted graph

Discrete structures like graphs make it possible to naturally and exibly model complex phenomena. Since graphs that represent various types of information are increasingly available today, their analysis has become a popular subject of research. The graphs studied in the field of data science at this time generally have a large number of nodes that are not fairly weighted and connected to each other, translating a structural specification of the data. Yet, even an algorithm for locating the average position in graphs is lacking although this knowledge would be of primary interest for statistical or representation problems. In this work, we develop a stochastic algorithm for finding the Fréchet mean of weighted undirected metric graphs. This method relies on a noisy simulated annealing algorithm dealt with using homogenization. We then illustrate our algorithm with two examples (subgraphs of a social network and of a collaboration and citation network)

From homogeneous to fractal normal and tumorous microvascular networks in the brain

We studied normal and tumorous three-dimensional (3D) microvascular networks in primate and rat brain. Tissues were prepared following a new preparation technique intended for high-resolution synchrotron tomography of microvascular networks. The resulting 3D images with a spatial resolution of less than the minimum capillary diameter permit a complete description of the entire vascular network for volumes as large as tens of cubic millimeters. The structural properties of the vascular networks were investigated by several multiscale methods such as fractal and power- spectrum analysis. These investigations gave a new coherent picture of normal and pathological complex vascular structures. They showed that normal cortical vascular networks have scale- invariant fractal properties on a small scale from 1.4 lm up to 40 to 65 lm. Above this threshold, vascular networks can be considered as homogeneous. Tumor vascular networks show similar characteristics, but the validity range of the fractal regime extend to much larger spatial dimensions. These 3D results shed new light on previous two dimensional analyses giving for the first time a direct measurement of vascular modules associated with vessel-tissue surface exchange