Transformation of a grid of quadrats to cope with perspective artifacts

The direct superimposition of a standard test grid of congruent quadrats onto an image bearing a population of particles exhibiting perspective artifacts, tends to increase the variance of the population size estimator, because the quadrat contents become unbalanced. If the quadrats are transformed according to the same projection mechanism affecting the particles, however, then the variance is restored into moderate values. Our purpose was to provide exact, easily programmable equations for the relevant transform

On the precisión of the nucleator

Abstract The nucleator is a design unbiased method of local stereology for estimating the volume of a bounded object. The only information required lies in the intersection of the object with an isotropic random ray emanating from a fixed point (called the pivotal point) associated with the object. For instance, the volume of a neuron can be estimated from a random ray emanating from its nucleolus. The nucleator is extensively used in biosciences because it is efficient and easy to apply. The estimator variance can be reduced by increasing the number of rays. In an earlier paper a systematic sampling design was proposed, and theoretical variance predictors were derived, for the corresponding volume estimator. Being the only variance predictors hitherto available for the nucleator, our basic goal was to check their statistical performance by means of Monte Carlo resampling on computer reconstructions of real objects. As a plus, the empirical distribution of the volume estimator revealed statistical properties of practical relevance

On the precision of the isotropic Cavalieri design

ABSTRACT: The isotropic Cavalieri design is based on a isotropically oriented set of parallel systematic sections a constant distance apart. Its advantage over the ordinary Cavalieri design is twofold - first, besides volume it allows the unbiased estimation of surface area, and second, the error variance predictor for the volume estimator is much simpler, involving only the surface area of the object, and the distance between sections. In an earlier paper, the two hemispheres of a rat brain were arranged perpendicular to each other before sectioning, aiming at reducing the error variance with respect to other arrangements (such as the aligned one) by exploiting an intuitively plausible antithetic effect. Because the total surface area of the objects is unchanged under any arrangements, however, the error variance predictor for the volume estimator does not depend on object shape, which looks intriguing. Using reconstructions of the mentioned hemispheres, we dilucidate the aparent paradox by means of automatic Monte Carlo replications of the relevant volume estimates under the antithetic and the aligned arrangements.The authors acknowledge financial support from the Spanish project AYA2015-66357-R (MINECO/FEDER)

Variance prediction for population size estimation

Design unbiased estimation of population size by stereological methods is an efficient alternative to automatic computer vision methods, which are generally biased. Moreover, stereological methods offer the possibility of predicting the error variance from a single sample. Here we explore the statistical performance of two alternative variance estimators on a dataset of 26 labelled crowd pictures. The empirical mean square errors of the variance predictors are compared by means of Monte Carlo resampling

Evaluating the pharmacological response in fluorescence microscopy images: The Δm algorithm

Current drug discovery procedures require fast and effective quantification of the pharmacological response evoked in living cells by agonist compounds. In the case of G-protein coupled receptors (GPCRs), the efficacy of a particular drug to initiate the endocytosis process is related to the formation of endocytic vesicles or endosomes and their subsequent internalisation within intracellular compartments that can be observed with high spatial and temporal resolution by fluorescence microscopy techniques. Recently, an algorithm has been proposed to evaluate the pharmacological response by estimating the number of endosomes per cell on time series of images. However, the algorithm was limited by the dependence on some manually set parameters and in some cases the quality of the image does not allow a reliable detection of the endosomes. Here we propose a simple, fast and automated image analysis method?the ?m algorithm- to quantify a pharmacological response with data obtained from fluorescence microscopy experiments. This algorithm does not require individual object detection and computes the relative increment of the third order moment in fluorescence microscopy images after filtering with the Laplacian of Gaussian function. It was tested on simulations demonstrating its ability to discriminate different experimental situations according to the number and the fluorescence signal intensity of the simulated endosomes. Finally and in order to validate this methodology with real data, the algorithm was applied to several time-course experiments based on the endocytosis of the mu opioid receptor (MOP) initiated by different agonist compounds. Each drug displayed a different ?m sigmoid time-response curve and statistically significant differences were observed among drugs in terms of efficacy and kinetic parameters

Simplified procedure for efficient and unbiased population size estimation

ABSTRACT: Population size estimation is relevant to social and ecological sciences. Exhaustive manual counting, the density method and automated computer vision are some of the estimation methods that are currently used. Some of these methods may work in concrete cases but they do not provide a fast, efficient and unbiased estimation in general. Recently, the CountEm method, based on systematic sampling with a grid of quadrats, was proposed. It offers an unbiased estimation that can be applied to any population. However, choosing suitable grid parameters is sometimes cumbersome. Here we define a more intuitive grid parametrization, using initial number of quadrats and sampling fraction. A crowd counting dataset with 51 images and their corresponding, manually annotated position point patterns, are used to analyze the variation of the coefficient of error with respect to different parameter choices. Our Monte Carlo resampling results show that the error depends on the sample size and the number of nonempty quadrats, but not on the size of the target population. A procedure to choose suitable parameter values is described, and the expected coefficients of error are given. Counting about 100 particles in 30 nonempty quadrats usually yields coefficients of error below 10%.This work was supported by AYA-2015-66357-R Ministerio de Economía, Industria y Competitividad (MINECO) / Fondos Europeos de Desarrollo Regional (FEDER) to MC

Método de estimación del número de partículas en un lugar determinado a partir de una imagen con perspectiva

Método para la estimación del número de partículas de una población en un lugar determinado a partir de una imagen con perspectiva, que comprende las etapas de: - obtener una imagen auxiliar sin perspectiva; - identificar y acotar en la imagen auxiliar el lugar en el que se encuentran las partículas en la imagen con perspectiva; - superponer de forma aleatoria una rejilla de ventanas de muestreo en la imagen auxiliar acotada; - tomar una pluralidad de puntos de contorno en cada ventana de muestreo, y con ecuaciones de proyección trasladar cada uno de dichos puntos a la imagen con perspectiva; - unir en la imagen con perspectiva los puntos trasladados del contorno de cada ventana y formar una nueva rejilla de ventanas de muestreo; - contar manualmente en la imagen con perspectiva el número total Q de partículas capturadas por la rejilla proyectada de ventanas de muestreo.Solicitud: 201700441 (29.03.2017)Nº Pub. de Solicitud: ES2643138A1 (21.11.2017

Using CMB polarization to constrain the anomalous nature of the Cold Spot with an incomplete-sky coverage

Recent results of the ESA Planck satellite have confirmed the existence of some anomalies in the statistical distribution of the cosmic microwave background (CMB) anisotropies. One of the most intriguing anomalies is the cold spot, first detected in the Wilkinson Microwave Anisotropy Probe (WMAP) data by Vielva et al. In a later paper, Vielva et al. (2011) developed a method to probe the anomalous nature of the cold spot by using the cross-correlation of temperature and polarization of the CMB fluctuations. Whereas this work was built under the assumption of analysing full-sky data, in this paper we extend such approach to deal with realistic data sets with a partial-sky coverage. In particular, we exploit the radial and tangential polarization patterns around temperature spots. We explore the capacity of the method to distinguish between a standard Gaussian CMB scenario and an alternative one, in which the cold spot arises from a physical process that does not present correlated polarization features (e.g. topological defects), as a function of the instrumental-noise level. Moreover, we consider more in detail the case of an ideal noise-free experiment and the ones with the expected instrumental-noise levels in QUIJOTE and Planck experiments. We also present an application to the 9-year WMAP data, without being able to obtain firm conclusions, with a significance level of 32 per cent. In the ideal case, the alternative scenario could be rejected at a significance level of around 1 per cent, whereas for expected noise levels of QUIJOTE and Planck experiments the corresponding significance levels are 1.5 and 7.4 per cent, respectively

Lipid Oxidation Inhibition in Frozen Farmed Salmon (Oncorhynchus kisutch ): Effect of Packaging

3 pages, 1 table.Coho salmon (Oncorhynchus kisutch) has recently attracted a great interest as a farmed product. This research focuses on its commercialisation as a frozen product. For it, an advanced storage technology combining vacuum and a polyphenolic rich-film was applied for a 9-months storage period (–18°C). The study was addressed to lipid hydrolysis and oxidation changes and to endogenous antioxidant content in salmon muscle. No effect of packaging conditions could be observed on free fatty acid formation. However, vacuum packaging conditions provided a partial inhibition of primary (peroxide) and secondary (anisidine value) lipid oxidation development; this inhibitory effect was accompanied by a lower tocopherol isomers loss. The employment of a film including polyphenolic compounds led to a partial inhibition of α-tocopherol breakdown and to a lower secondary (anisidine value) and tertiary (fluorescent compound formation) lipid oxidation development. A partial inhibitory effect on lipid oxidation development is concluded for the employment of a polyphenolic compound rich-film packaging when applied to farmed coho salmon.This research was carried out in the frame of the Project No. 2006 CL 0034 (2007–2008), granted by the U. Chile-CSIC Cooperation Program. Coho salmon fish was provided by Aquachile SA (Puerto Montt, Chile).Peer reviewe

Physical activity phenotypes and mortality in older adults: a novel distributional data analysis of accelerometry in the NHANES

Physical activity is deemed critical to successful ageing. Despite evidence and progress, there is still a need to determine more precisely the direction, magnitude, intensity, and volume of physical activity that should be performed on a daily basis to effectively promote the health of individuals. This study aimed to assess the clinical validity of new physical activity phenotypes derived from a novel distributional functional analysis of accelerometer data in older adults. A random sample of participants aged between 65 and 80 years with valid accelerometer data from the National Health and Nutrition Examination Survey (NHANES) 2011–2014 was used. Five major clinical phenotypes were identified, which provided a greater sensitivity for predicting 5-year mortality and survival outcomes than age alone, and our results confirm the importance of moderate-to-vigorous physical activity. The new clinical physical activity phenotypes are a promising tool for improving patient prognosis and for directing to more targeted intervention planning, according to the principles of precision medicine. The use of distributional representations shows clear advantages over more traditional metrics to explore the effects of the full spectrum of the physical activity continuum on human healthOpen Access funding provided thanks to the CRUE-CSIC agreement with Springer Nature. This research was funded by the Ministry of Science and Innovation of Spain, under Grant No. PID2021-123152OB-C21S