Multi Focus Image Fusion with variable size windows

[EN] In this paper we present the Linear Image Combination Algorithm with Variable Windows (CLI-VV) for the fusion of multifocus images. Unlike the CLI-S algorithm presented in a previous work, the CLI-VV algorithm allows to automatically determine the optimal size of the window in each pixel for the segmentation of the regions with the highest sharpness. We also present the generalized CLI-VV Algorithm for the fusion of sets of multi-focus images with more than two images. This new algorithm is called Variable Windows Multi-focus Fusion (FM-VV). The CLI-VV Algorithm was tested with 21 pairs of synthetic images and 29 pairs of real multi-focus images, and the FM-VV Algorithm on 5 trios of multi-focus images. In all the tests a competitive accuracy was obtained, with execution times lower than those reported in the literature.[ES] En este artículo presentamos el Algoritmo Combinación Lineal de Imágenes con Ventanas Variables (CLI-VV) para la fusión de imágenes multi-foco. A diferencia del Algoritmo CLI-S presentado en un trabajo anterior, el algoritmo CLI-VV permite determinar automáticamente el tamaño óptimo de la ventana en cada píxel para la segmentación de las regiones con la mayor nitidez. También presentamos la generalizado el Algoritmo CLI-VV para la fusión de conjuntos de imágenes multi-foco con más de dos imágenes. A este nuevo algoritmo lo denominamos Fusión Multi-foco con Ventanas Variables (FM-VV). El Algoritmo CLI-VV se probó con 21 pares de imágenes sintéticas y 29 pares de imágenes multi-foco reales, y el Algoritmo FM-VV sobre 5 tríos de imágenes multi-foco. En todos los ejemplos se obtuvo un porcentaje de acierto competitivos, producidos en tiempos de ejecución menores a los reportados en la literatura.Calderon, F.; Garnica-Carrillo, A.; Flores, JJ. (2018). Fusión de Imágenes Multi-Foco con Ventanas Variables. 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Ontogenetic changes in cutaneous and branchial ionocytes and morphology in yellowfin tuna (Thunnus albacares) larvae.

The development of osmoregulatory and gas exchange organs was studied in larval yellowfin tuna (Thunnus albacares) from 2 to 25 days post-hatching (2.9-24.5 mm standard length, SL). Cutaneous and branchial ionocytes were identified using Na+/K+-ATPase immunostaining and scanning electron microscopy. Cutaneous ionocyte abundance significantly increased with SL, but a reduction in ionocyte size and density resulted in a significant decrease in relative ionocyte area. Cutaneous ionocytes in preflexion larvae had a wide apical opening with extended microvilli; however, microvilli retracted into an apical pit from flexion onward. Lamellae in the gill and pseudobranch were first detected ~ 3.3 mm SL. Ionocytes were always present on the gill arch, first appeared in the filaments and lamellae of the pseudobranch at 3.4 mm SL, and later in gill filaments at 4.2 mm SL, but were never observed in the gill lamellae. Unlike the cutaneous ionocytes, gill and pseudobranch ionocytes had a wide apical opening with extended microvilli throughout larval development. The interlamellar fusion, a specialized gill structure binding the lamellae of ram-ventilating fish, began forming by ~ 24.5 mm SL and contained ionocytes, a localization never before reported. Ionocytes were retained on the lamellar fusions and also found on the filament fusions of larger sub-adult yellowfin tuna; however, sub-adult gill ionocytes had apical pits. These results indicate a shift in gas exchange and NaCl secretion from the skin to branchial organs around the flexion stage, and reveal novel aspects of ionocyte localization and morphology in ram-ventilating fishes

Variational Methods for Biomolecular Modeling

Structure, function and dynamics of many biomolecular systems can be characterized by the energetic variational principle and the corresponding systems of partial differential equations (PDEs). This principle allows us to focus on the identification of essential energetic components, the optimal parametrization of energies, and the efficient computational implementation of energy variation or minimization. Given the fact that complex biomolecular systems are structurally non-uniform and their interactions occur through contact interfaces, their free energies are associated with various interfaces as well, such as solute-solvent interface, molecular binding interface, lipid domain interface, and membrane surfaces. This fact motivates the inclusion of interface geometry, particular its curvatures, to the parametrization of free energies. Applications of such interface geometry based energetic variational principles are illustrated through three concrete topics: the multiscale modeling of biomolecular electrostatics and solvation that includes the curvature energy of the molecular surface, the formation of microdomains on lipid membrane due to the geometric and molecular mechanics at the lipid interface, and the mean curvature driven protein localization on membrane surfaces. By further implicitly representing the interface using a phase field function over the entire domain, one can simulate the dynamics of the interface and the corresponding energy variation by evolving the phase field function, achieving significant reduction of the number of degrees of freedom and computational complexity. Strategies for improving the efficiency of computational implementations and for extending applications to coarse-graining or multiscale molecular simulations are outlined.Comment: 36 page

Clustering and dynamics of cytochrome bd-I complexes in the Escherichia coli plasma membrane in vivo

The definitive version is available at www3.interscience.wiley.co

Characterization of Transport and Adsorption Mechanisms in Chromatographic Media

This work deals with experimentally determined binding orientations of lysozyme on different chromatographic adsorber materials at varying mobile phase compositions (ionic strength and pH). Findings were correlated with molecular dynamics simulations and used to obtain a model approach to predict protein retention times in ion-exchange chromatography. The second part of this work deals with confocal laser-scanning microscopy as a tool to visualize protein transpiort in chromatographic media

Time-resolved FRET fluorescence spectroscopy of visible fluorescent protein pairs

Förster resonance energy transfer (FRET) is a powerful method for obtaining information about small-scale lengths between biomacromolecules. Visible fluorescent proteins (VFPs) are widely used as spectrally different FRET pairs, where one VFP acts as a donor and another VFP as an acceptor. The VFPs are usually fused to the proteins of interest, and this fusion product is genetically encoded in cells. FRET between VFPs can be determined by analysis of either the fluorescence decay properties of the donor molecule or the rise time of acceptor fluorescence. Time-resolved fluorescence spectroscopy is the technique of choice to perform these measurements. FRET can be measured not only in solution, but also in living cells by the technique of fluorescence lifetime imaging microscopy (FLIM), where fluorescence lifetimes are determined with the spatial resolution of an optical microscope. Here we focus attention on time-resolved fluorescence spectroscopy of purified, selected VFPs (both single VFPs and FRET pairs of VFPs) in cuvette-type experiments. For quantitative interpretation of FRET–FLIM experiments in cellular systems, details of the molecular fluorescence are needed that can be obtained from experiments with isolated VFPs. For analysis of the time-resolved fluorescence experiments of VFPs, we have utilised the maximum entropy method procedure to obtain a distribution of fluorescence lifetimes. Distributed lifetime patterns turn out to have diagnostic value, for instance, in observing populations of VFP pairs that are FRET-inactiv