VIOLA - A multi-purpose and web-based visualization tool for neuronal-network simulation output

Neuronal network models and corresponding computer simulations are invaluable tools to aid the interpretation of the relationship between neuron properties, connectivity and measured activity in cortical tissue. Spatiotemporal patterns of activity propagating across the cortical surface as observed experimentally can for example be described by neuronal network models with layered geometry and distance-dependent connectivity. The interpretation of the resulting stream of multi-modal and multi-dimensional simulation data calls for integrating interactive visualization steps into existing simulation-analysis workflows. Here, we present a set of interactive visualization concepts called views for the visual analysis of activity data in topological network models, and a corresponding reference implementation VIOLA (VIsualization Of Layer Activity). The software is a lightweight, open-source, web-based and platform-independent application combining and adapting modern interactive visualization paradigms, such as coordinated multiple views, for massively parallel neurophysiological data. For a use-case demonstration we consider spiking activity data of a two-population, layered point-neuron network model subject to a spatially confined excitation originating from an external population. With the multiple coordinated views, an explorative and qualitative assessment of the spatiotemporal features of neuronal activity can be performed upfront of a detailed quantitative data analysis of specific aspects of the data. Furthermore, ongoing efforts including the European Human Brain Project aim at providing online user portals for integrated model development, simulation, analysis and provenance tracking, wherein interactive visual analysis tools are one component. Browser-compatible, web-technology based solutions are therefore required. Within this scope, with VIOLA we provide a first prototype.Comment: 38 pages, 10 figures, 3 table

Robust visualization and discrimination of nanoparticles by interferometric imaging

Single-molecule and single-nanoparticle biosensors are a growing frontier in diagnostics. Digital biosensors are those which enumerate all specifically immobilized biomolecules or biological nanoparticles, and thereby achieve limits of detection usually beyond the reach of ensemble measurements. Here we review modern optical techniques for single nanoparticle detection and describe the single-particle interferometric reflectance imaging sensor (SP-IRIS). We present challenges associated with reliably detecting faint nanoparticles with SP-IRIS, and describe image acquisition processes and software modifications to address them. Specifically, we describe a image acquisition processing method for the discrimination and accurate counting of nanoparticles that greatly reduces both the number of false positives and false negatives. These engineering improvements are critical steps in the translation of SP-IRIS towards applications in medical diagnostics.R01 AI096159 - NIAID NIH HHSFirst author draf

Correlation Plenoptic Imaging With Entangled Photons

Plenoptic imaging is a novel optical technique for three-dimensional imaging in a single shot. It is enabled by the simultaneous measurement of both the location and the propagation direction of light in a given scene. In the standard approach, the maximum spatial and angular resolutions are inversely proportional, and so are the resolution and the maximum achievable depth of focus of the 3D image. We have recently proposed a method to overcome such fundamental limits by combining plenoptic imaging with an intriguing correlation remote-imaging technique: ghost imaging. Here, we theoretically demonstrate that correlation plenoptic imaging can be effectively achieved by exploiting the position-momentum entanglement characterizing spontaneous parametric down-conversion (SPDC) photon pairs. As a proof-of-principle demonstration, we shall show that correlation plenoptic imaging with entangled photons may enable the refocusing of an out-of-focus image at the same depth of focus of a standard plenoptic device, but without sacrificing diffraction-limited image resolution.Comment: 12 pages, 5 figure

Surface-to-Bulk Redox Coupling through Thermally Driven Li Redistribution in Li- and Mn-Rich Layered Cathode Materials.

Li- and Mn-rich (LMR) layered cathode materials have demonstrated impressive capacity and specific energy density thanks to their intertwined redox centers including transition metal cations and oxygen anions. Although tremendous efforts have been devoted to the investigation of the electrochemically driven redox evolution in LMR cathode at ambient temperature, their behavior under a mildly elevated temperature (up to ∼100 °C), with or without electrochemical driving force, remains largely unexplored. Here we show a systematic study of the thermally driven surface-to-bulk redox coupling effect in charged Li1.2Ni0.15Co0.1Mn0.55O2. We for the first time observed a charge transfer between the bulk oxygen anions and the surface transition metal cations under ∼100 °C, which is attributed to the thermally driven redistribution of Li ions. This finding highlights the nonequilibrium state and dynamic nature of the LMR material at deeply delithiated state upon a mild temperature perturbation

Practical acquisition and rendering of diffraction effects in surface reflectance

We propose two novel contributions for measurement based rendering of diffraction effects in surface reflectance of planar homogeneous diffractive materials. As a general solution for commonly manufactured materials, we propose a practical data-driven rendering technique and a measurement approach to efficiently render complex diffraction effects in real-time. Our measurement step simply involves photographing a planar diffractive sam- ple illuminated with an LED flash. Here, we directly record the resultant diffraction pattern on the sample surface due to a narrow band point source illumination. Furthermore, we propose an efficient rendering method that exploits the measurement in conjunction with the Huygens-Fresnel principle to fit relevant diffraction parameters based on a first order approximation. Our proposed data-driven rendering method requires the precomputation of a single diffraction look up table for accurate spectral rendering of com- plex diffraction effects. Secondly, for sharp specular samples, we propose a novel method for practical measurement of the underlying diffraction grating using out-of-focus “bokeh” photography of the specular highlight. We demonstrate how the measured bokeh can be employed as a height field to drive a diffraction shader based on a first order approximation for efficient real-time rendering. Finally, we also drive analytic solutions for a few special cases of diffraction from our measurements and demonstrate realistic rendering results under complex light sources and environments