Circular Blob Research Articles

Automation of Caenorhabditis elegans lifespan assay using a simplified domain synthetic image-based neural network training strategy

Performing lifespan assays with Caenorhabditis elegans (C. elegans) nematodes manually is a time consuming and laborious task. Therefore, automation is necessary to increase productivity. In this paper, we propose a method to automate the counting of live C. elegans using deep learning. The survival curves of the experiment are obtained using a sequence formed by an image taken on each day of the assay. Solving this problem would require a very large labeled dataset; thus, to facilitate its generation, we propose a simplified image-based strategy. This simplification consists of transforming the real images of the nematodes in the Petri dish to a synthetic image, in which circular blobs are drawn on a constant background to mark the position of the C. elegans. To apply this simplification method, it is divided into two steps. First, a Faster R-CNN network detects the C. elegans, allowing its transformation into a synthetic image. Second, using the simplified image sequence as input, a regression neural network is in charge of predicting the count of live nematodes on each day of the experiment. In this way, the counting network was trained using a simple simulator, avoiding labeling a very large real dataset or developing a realistic simulator. Results showed that the differences between the curves obtained by the proposed method and the manual curves are not statistically significant for either short-lived N2 (p-value log rank test 0.45) or long-lived daf-2 (p-value log rank test 0.83) strains.

A Scale Normalized Generalized LoG Detector Approach for Retinal Vessel Segmentation

Retinal vessel segmentation is important for analyzing many retinal diseases, where manual segmentation of these vessels is an extensive job. Automatic segmentation of these vessels can help much in the diagnosis of these retinal diseases. Several image processing schemes that are considering the retinal vessel segmentation are lacking in segmentation performance and robustness. Laplacian of Gaussian (LoG) detectors is a popular choice method for edge detection adapted for detecting circular blob detection. Laplacian kernel approximates the second-order derivative to the image, which can be effective in combination with Gaussian smoothing in the form of LoG. The LoG detectors are famous for good border detection in noisy images. Based on their parameter, their behavior can be switched between ridge or blob detection. However, their performance generally falls off for elliptical blobs. A generalized LoG detector was proposed recently to deal with elliptical blob detection. Comparing simulation studies for the second-order ridge detector with other popular ridge detectors provides evidence of its effectiveness. The proposed ridge detector shows promise when applied to detect vessels in real-world retinal images of a publicly available database. The method's capabilities are evaluated with a comparison of state of the art, and the performances are obtained on the database most used by researchers. The DRIVE,STARE and CHASE_DB1 databases are used for performance evaluation, and we achieved a sensitivity of 0.785, a specificity of 0.967 and an accuracy of 0.952 on the DRIVE database,a sensitivity of 0.788, a specificity of 0.966 and a precision of 0.951 and a sensitivity of 0.787, a specificity of 0.968 and a precision of 0.952 on CHASE_DB1.

An Automated Method for Detection and Enumeration of Olive Trees Through Remote Sensing

Country olive forests are one of the major contributors with economic aspects. Spain is the leading country in the world which produced around 45% of olive oil compared to the total production in the world. The value of 2.4 million hectares of land is dedicated to olive cultivation in the country, which made it a huge olive oil producer in the world. Olive crop widely spread over large extensive areas; manual counting of trees is humanly infeasible. To address this problem, we propose an automatic scheme for the detection and enumeration of olive trees. The proposed technique comprises of multi-step image processing techniques applied over a single band of imagery. The single red band once extracted from the color spectrum of acquired images, is then sharpened and edges are detected. The closed edges formed by the tree boundaries are transformed into white blobs using morphological reconstruction. Resulting circular blobs are then filtered out based on their shape and size. Blobs with circular geometry and in-range radius are considered as olive trees, which are then mapped with the existing ground information. Results have been generated over the diverse images capturing the ground truth information with an estimation error of 1.27%.

Structural transformation and property improvement of Fe78Si9B13 amorphous ribbon by pulsed laser processing

The effects of pulsed laser processing (PLP) with different laser power (PL = 10, 20 and 30 W) on the surface morphology, structure and properties of Fe78Si9B13 amorphous ribbon were investigated. It was found that the circular blobs, convex in perimeter and sunk in middle, distributed regularly on the surface of ribbon after PLP with PL = 10 W. As PL increased to 20 and 30 W, obvious splashes occurred around the laser blobs. On the surface of ribbons after PLP, fresh amorphous structures were generated, which were confirmed by small angle X-ray scattering and transmission electron microscope data. Meanwhile, a small number of nanocrystallines formed at heat affected zone. The X-ray diffraction results indicated that the transformation from fcc to bcc SRO structure units occurred during PLP, resulting in a lower characteristic distance δC. The pitting resistance, soft magnetic property and thermal stability of ribbons were enhanced after PLP. Especially, the properties had a significant improvement with increasing PL from 10 to 20 W, but had a slight deterioration as PL increased further from 20 to 30 W. Overall, an optimal laser power of 20 W was obtained for PLP of Fe78Si9B13 amorphous ribbon in this work.

Deriving scale normalisation factors for a GLoG detector

In computer vision, blob detection is used to obtain regions of interest that could signal the presence of objects or parts with application to object recognition and object tracking. One of the more common blob detectors is based on the Laplacian of Gaussian (LoG). However, most blob detectors developed in the past assume circular blobs, and these detectors do not perform as well with elliptical blobs, a more prevalent scenario in real images. A generalised LoG (GLoG) detector was proposed recently to deal specifically with elliptical blobs. To formulate the GLoG in a multi-scale framework, its response must be made scale invariant. Toward that end, necessary and sufficient conditions are presented here, with the normalisation factors derived for a scale-invariant GLoG detector. The factors are validated with a synthetic example and are further tested with two real-world images.

Remote Sensing: An Automated Methodology for Olive Tree Detection and Counting in Satellite Images

Cultivation of olive trees for the past few years has been widely spread across Mediterranean countries, including Spain, Greece, Italy, France, and Turkey. Among these countries, Spain is listed as the largest olive producing country with almost 45% of olive oil production per year. Dedicating land of over 2.4 million hectares for the olive cultivation, Spain is among the leading distributors of olives throughout the world. Due to its high significance in the country’s economy, the crop yield must be recorded. Manual collection of data over such expanded fields is humanly infeasible. Remote collection of such information can be made possible through the utilization of satellite imagery. This paper presents an automated olive tree counting method based on image processing of satellite imagery. The images are pre-processed using the unsharp masking followed by improved multi-level thresholding-based segmentation. Resulting circular blobs are detected through the circular Hough transform for identification. Validation has been performed by evaluating the proposed scheme for the dataset formed by acquiring images through the “El Sistema de Informacion Geografica de Parcelas Agricolas” viewer over the region of Spain. The proposed algorithm achieves an accuracy of 96% in detection. Computation time was recorded as 24 ms for an image size of $300\times300$ pixels. The less spectral information is used in our proposed methodology resulting in a competitive accuracy with low computational cost in comparison to the state-of-the-art technique.

Dynamics of a Highly Viscous Circular Blob in Homogeneous Porous Media

Viscous fingering is ubiquitous in miscible displacements in porous media, in particular, oil recovery, contaminant transport in aquifers, chromatography separation, and geological CO2 sequestration. The viscosity contrasts between heavy oil and water is several orders of magnitude larger than typical viscosity contrasts considered in the majority of the literature. We use the finite element method (FEM)-based COMSOL Multiphysics simulator to simulate miscible displacements in homogeneous porous media with very large viscosity contrasts. Our numerical model is suitable for a wide range of viscosity contrasts covering chromatographic separation as well as heavy oil recovery. We have successfully captured some interesting and previously unexplored dynamics of miscible blobs with very large viscosity contrasts in homogeneous porous media. We study the effect of viscosity contrast on the spreading and the degree of mixing of the blob. Spreading (variance of transversely averaged concentration) follows the power law t 3 . 34 for the blobs with viscosity ∼ O ( 10 2 ) and higher, while degree of mixing is found to vary non-monotonically with log-mobility ratio. Moreover, in the limit of very large viscosity contrast, the circular blob behaves like an erodible solid body and the degree of mixing approaches the viscosity-matched case.

Expectations and visual aftereffects.

The tilt aftereffect (TAE) is traditionally regarded as a consequence of orientation-selective sensory adaptation, a low-level stimulus-driven process. Adaptation has been recently suggested to be the outcome of predictive coding. Here, we tested whether the TAE is modulated by predictability, and specifically, whether TAE depends on the congruency of adapted and expected orientations. Observers were presented with successive pairs of oriented Gabor patches. Pairs were arranged in blocks, forming two conditions with the orientation of the second pair member either predictable or not. For all pairs, the orientation of the first Gabor was tilted clockwise (CW) or counterclockwise (CCW) (±20° relative to vertical, randomized). In the "Expected" conditions, the orientation of the second Gabor was fixed relative to the first Gabor (the same or a mirror orientation, blocked). In the "no-expectation" condition, the orientation of the second Gabor was independent of the first Gabor (randomized ±20°). Intermixed test pairs were used to measure observers' perceived vertical, with the second pair member serving as a target, oriented around the vertical, permitting an estimate of the TAE produced by the presentation of the first Gabor. Results show an increase in TAE with the expected orientation matching the inducing orientation, but a decrease with the expected mirror orientation, consistent with additivity of the adaptation and the expectation effects. A second experiment, with the first oriented Gabor replaced by a colored circular blob, showed that expectation alone does not modulate the perceived orientation. These findings indicate a role for expectation in generating the perceptual TAE and are in line with predictive coding models of perception. We suggest that orientation dependent adaptation is affected by both the mean orientation (first order statistics) and by temporal contingencies (second order statistics).

Fingering instability and mixing of a blob in porous media.

The curvature of the unstable part of the miscible interface between a circular blob and the ambient fluid in two-dimensional homogeneous porous media depends on the viscosity of the fluids. The influence of the interface curvature on the fingering instability and mixing of a miscible blob within a rectilinear displacement is investigated numerically. The fluid velocity in porous media is governed by Darcy's law, coupled with a convection-diffusion equation that determines the evolution of the solute concentration controlling the viscosity of the fluids. Numerical simulations are performed using a Fourier pseudospectral method to determine the dynamics of a miscible blob (circular or square). It is shown that for a less viscous circular blob, there exist three different instability regions without any finite R-window for viscous fingering, unlike the case of a more viscous circular blob. Critical blob radius for the onset of instability is smaller for a less viscous blob as compared to its more viscous counterpart. Fingering enhances spreading and mixing of miscible fluids. Hence a less viscous blob mixes with the ambient fluid quicker than the more viscous one. Furthermore, we show that mixing increases with the viscosity contrast for a less viscous blob, while for a more viscous one mixing depends nonmonotonically on the viscosity contrast. For a more viscous blob mixing depends nonmonotonically on the dispersion anisotropy, while it decreases monotonically with the anisotropic dispersion coefficient for a less viscous blob. We also show that the dynamics of a more viscous square blob is qualitatively similar to that of a circular one, except the existence of the lump-shaped instability region in the R-Pe plane. We have shown that the Rayleigh-Taylor instability in a circular blob (heavier or lighter than the ambient fluid) is independent of the interface curvature.

Viscous fingering and deformation of a miscible circular blob in a rectilinear displacement in porous media

The deformation of an initially circular miscible blob in a rectilinear displacement is investigated numerically for porous media when the blob is more viscous than the displacing fluid. We find in the parameter space spanned by the Péclet number and log-mobility ratio the existence of a new lump-shaped instability zone between two distinct regimes of comet and viscous fingering (VF) deformations. The more viscous circular blob is destabilized by VF only over a finite window of log-mobility ratio, contrary to the displacement of a more viscous finite slice with planar interfaces. This difference is attributed to the initial curvature of the miscible blob.

Poisson growth

The two-dimensional free boundary problem in which the field is governed by Poisson’s equation and for which the velocity of the free boundary is given by the gradient of the field—Poisson growth—is considered. The problem is a generalisation of classic Hele-Shaw free boundary flow or Laplacian growth problem and has many applications. In the case when the right hand side of Poisson’s equation is constant, a formulation is obtained in terms of the Schwarz function of the free boundary. From this it is deduced that solutions of the Laplacian growth problem also satisfy the Poisson growth problem, the only difference being in their time evolution. The corresponding moment evolution equations, a Polubarinova–Galin type equation and a Baiocchi-type transformation for Poisson growth are also presented. Some explicit examples are given, one in which cusp formation is inhibited by the addition of the Poisson term, and another for a growing finger in which the Poisson term selects the width of the finger to be half that of the channel. For the more complicated case when the right hand side is linear in one space direction, the Schwarz function method is used to derive an exact solution describing a translating circular blob with changing radius.

Radial Hele-Shaw flow with suction: fully nonlinear pattern formation.

We study the development of intricate, fully nonlinear immiscible interfacial patterns in the suction-driven radial Hele-Shaw problem. The complex-shaped, contracting fluid-fluid interface arises when an initially circular blob of more viscous fluid, surrounded by less viscous one, is drawn into an eccentric point sink. We present sophisticated numerical simulations, based on a diffuse interface model, that capture the most prominent interfacial features revealed by existing experimental studies of the problem. The response of the system to changes in the capillary number is investigated, accurately revealing the occurrence of finger competition phenomena, and correctly describing the velocity behavior of both inward- and outward-pointing fingers. For the large-capillary-number regime, a set of complex interfacial features (finger merging, shielding, and pinch-off) whose experimental realization is still not available, are predicted.

Hele-Shaw flow driven by an electric field

The behaviour of two-dimensional finite blobs of conducting viscous fluid in a Hele-Shaw cell subject to an electric field is considered. The time-dependent free boundary problem is studied both analytically using the Schwarz function of the free boundary and numerically using a boundary integral method. Various problems are considered, including (i) the behaviour of an initially circular blob of conducting fluid subject to an electric point charge located arbitrarily within the blob, (ii) the delay in cusp formation on the free boundary in sink-driven flow due to a strategically placed electric charge and (iii) the stability of exact steady solutions having both hydrodynamic and electric forcing.

Modelling of urban growth boundary using geoinformatics

Urban growth boundary (UGB) is a regulatory measure of local government for delineating limits of urban growth over a period of time. Land within the UGB allows urban development, while the land outside of this boundary remains primarily non-urban. The increasing popularity of UGB demands an easy and effective method to design this boundary. This article introduces a new concept, Ideal Urban Radial Proximity (IURP), to designate a spatial UGB using geoinformatics in the digital environment. The Kolkata urban agglomeration was considered to demonstrate this model. Remotely sensed imageries of three temporal instants (years 1975, 1990 and 2005) were considered to determine the information on urban extent and growth of the city. These data were then used as inputs to model the UGB for the years 2020 and 2035. The proposed model discourages scattered development and increase in urban growth rate. It preserves urban vegetation, water bodies and any other important non-urban areas within the inner city space. The IURP concept will also be useful to make the cities circular and polycentric urban blobs into a monocentric tract. Apart from the proposed model and derived results, this research also proves the potential of geoinformatics in modelling a UGB.

Collisionality and magnetic geometry effects on tokamak edge turbulent transport. II. Many-blob turbulence in the two-region model

A two-region model, coupling the outboard midplane and the X-point region, was proposed in Paper I [J. R. Myra, D. A. Russell, and D. A. D’Ippolito, Phys. Plasmas 13, 112502 (2006)] to study the effects of collisionality and magnetic geometry on electrostatic turbulent transport in the edge and scrape-off layer of a diverted tokamak plasma by filamentary coherent structures or “blobs.” Attention was focused on the properties of isolated blobs. That study is extended here to the many-blob, turbulent saturated state driven by a linearly unstable density profile. The evolution of the density profile is included. It is demonstrated that turbulent density transport increases with collisionality but decreases with enhanced magnetic field-line fanning and shear in this model. Field-line shear induces poloidal velocity in isolated blob propagation and de-correlates the electrostatic potentials in the two regions in the turbulent regime. Probability density functions of density flux resemble those of experimental probe data: both are insensitive to magnetic field geometry and collisionality. It is shown that blobs are born where the skewness of density fluctuations vanishes and the logarithmic pressure gradient is maximized. The simulations show increased particle fluxes with increased plasma resistivity, which are due to increases in both blob velocity and creation rate (or spatial “packing fraction”). A wavelet-type Gaussian-fitting analysis is used to study the dependence of blob velocity on blob size. It is found that streamers, which dominate the simulations, move faster than circular blobs when the two regions are electrically disconnected.

Thermophysical properties of high porosity metal foams

In this paper, we present a comprehensive analytical and experimental investigation for the determination of the effective thermal conductivity ( k e), permeability ( K) and inertial coefficient ( f) of high porosity metal foams. In the first part of the study, we provide an analysis for estimating the effective thermal conductivity ( k e). Commercially available metal foams form a complex array of interconnected fibers with an irregular lump of metal at the intersection of two fibers. In our theoretical model, we represent this structure by a model consisting of a two-dimensional array of hexagonal cells where the fibers form the sides of the hexagons. The lump is taken into account by considering a circular blob of metal at the intersection. The analysis shows that k e depends strongly on the porosity and the ratio of the cross-sections of the fiber and the intersection. However, it has no systematic dependence on pore density. Experimental data with aluminum and reticulated vitreous carbon (RVC) foams, using air and water as fluid media are used to validate the analytical predictions. The second part of our paper involves the determination of the permeability ( K) and inertial coefficient ( f) of these high porosity metal foams. Fluid flow experiments were conducted on a number of metal foam samples covering a wide range of porosities and pore densities in our in-house wind tunnel. The results show that K increases with pore diameter and porosity of the medium. The inertial coefficient, f, on the other hand, depends only on porosity. An analytical model is proposed to predict f based on the theory of flow over bluff bodies, and is found to be in excellent agreement with the experimental data. A modified permeability model is also presented in terms of the porosity, pore diameter and tortuosity of our metal foam samples, and is shown to be in reasonable agreement with measured data.

Numerical study of Hele-Shaw flow with suction

We investigate numerically the effects of surface tension on the evolution of an initially circular blob of viscous fluid in a Hele-Shaw cell. The blob is surrounded by less viscous fluid and is drawn into an eccentric point sink. In the absence of surface tension, these flows are known to form cusp singularities in finite time. Our study focuses on identifying how these cusped flows are regularized by the presence of small surface tension, and what the limiting form of the regularization is as surface tension tends to zero. The two-phase Hele-Shaw flow, known as the Muskat problem, is considered. We find that, for nonzero surface tension, the motion continues beyond the zero-surface-tension cusp time, and generically breaks down only when the interface touches the sink. When the viscosity of the surrounding fluid is small or negligible, the interface develops a finger that bulges and later evolves into a wedge as it approaches the sink. A neck is formed at the top of the finger. Our computations reveal an asymptotic shape of the wedge in the limit as surface tension tends to zero. Moreover, we find evidence that, for a fixed time past the zero-surface-tension cusp time, the vanishing surface tension solution is singular at the finger neck. The zero-surface-tension cusp splits into two corner singularities in the limiting solution. Larger viscosity in the exterior fluid prevents the formation of the neck and leads to the development of thinner fingers. It is observed that the asymptotic wedge angle of the fingers decreases as the viscosity ratio is reduced, apparently towards the zero angle (cusp) of the zero-viscosity-ratio solution.

Sensitivity to modulations of luminance and contrast in visual white noise: separate mechanisms with similar behaviour

Human vision can detect spatiotemporal information conveyed by first-order modulations of luminance and by second-order, non-Fourier modulations of image contrast. Models for second-order motion have suggested two filtering stages separated by a rectifying nonlinearity. We explore here the encoding of stationary first-order and second-order gratings, and their interaction. Stimuli consisted of 2-D binary, broad-band, static, visual noise sinusoidally modulated in luminance (LM, first-order) or contrast (CM, second-order). Modulation thresholds were measured in a two-interval forced-choice staircase procedure. Sensitivity curves for LM and CM had similar shape as a function of spatial frequency, and as a function of the size of a circular Gaussian blob of modulation. Weak background gratings present in both intervals produced order-specific facilitation: LM background facilitated LM detection (the dipper function) and CM facilitated CM detection. LM did not facilitate CM, nor vice-versa, neither in-phase nor out-of-phase, and this is strong evidence that LM and CM are detected via separate mechanisms. This conclusion was further supported by an experiment on the detection of LM/CM mixtures. From a general mathematical model and a specific computer simulation we conclude that a single mechanism sensitive to both LM and CM cannot predict the pattern of results for mixtures, while a model containing separate pathways for LM and CM, followed by energy summation, does so successfully and is quantitatively consistent with the finding of order-specific facilitation.

Chaotic mixing of granular materials in two-dimensional tumbling mixers.

We consider the mixing of similar, cohesionless granular materials in quasi-two-dimensional rotating containers by means of theory and experiment. A mathematical model is presented for the flow in containers of arbitrary shape but which are symmetric with respect to rotation by 180 degrees and half-filled with solids. The flow comprises a thin cascading layer at the flat free surface, and a fixed bed which rotates as a solid body. The layer thickness and length change slowly with mixer rotation, but the layer geometry remains similar at all orientations. Flow visualization experiments using glass beads in an elliptical mixer show good agreement with model predictions. Studies of mixing are presented for circular, elliptical, and square containers. The flow in circular containers is steady, and computations involving advection alone (no particle diffusion generated by interparticle collisions) show poor mixing. In contrast, the flow in elliptical and square mixers is time periodic and results in chaotic advection and rapid mixing. Computational evidence for chaos in noncircular mixers is presented in terms of Poincare sections and blob deformation. Poincare sections show regions of regular and chaotic motion, and blobs deform into homoclinic tendrils with an exponential growth of the perimeter length with time. In contrast, in circular mixers, the motion is regular everywhere and the perimeter length increases linearly with time. Including particle diffusion obliterates the typical chaotic structures formed on mixing; predictions of the mixing model including diffusion are in good qualitative and quantitative (in terms of the intensity of segregation variation with time) agreement with experimental results for mixing of an initially circular blob in elliptical and square mixers. Scaling analysis and computations show that mixing in noncircular mixers is faster than that in circular mixers, and the difference in mixing times increases with mixer size. (c) 1999 American Institute of Physics.

Discrete vortex simulation of the separated flow around a rotating circular cylinder at high Reynolds number

The separated flow around a rotating circular cylinder is investigated by the discrete vortex method combined with the boundary layer theory. The Keller Box method is used to solve the laminar boundary layer in order to determine the separation points on the upper and the lower sides of the rotating circular cylinder. The nascent vortices are then introduced near the separation points. A discrete circular vortex blob model, which has uniform vorticity distribution, is adopted to simulate the unsteady wake. Numerical experiments are conducted to investigate the cases in which the ratio of the speed at the cylinder surface to the speed at infinity is varied from 0 to 0.3 at a Reynolds number of 6 × 10 3. The calculated values of the separation positions, the drag and lift force coefficients, the velocuty and the pressure distribution on the cylinder surface are found to agree well with the published experimental data.