The Lattice-Boltzmann Method on Optimal Sampling Lattices

In this paper, we extend the single relaxation time Lattice-Boltzmann Method (LBM) to the 3D body-centered cubic (BCC) lattice. We show that the D3bQ15 lattice defined by a 15 neighborhood connectivity of the BCC lattice is not only capable of more accurately discretizing the velocity space of the continuous Boltzmann equation as compared to the D3Q15 Cartesian lattice, it also achieves a comparable spatial discretization with 30 percent less samples. We validate the accuracy of our proposed lattice by investigating its performance on the 3D lid-driven cavity flow problem and show that the D3bQ15 lattice offers significant cost savings while maintaining a comparable accuracy. We demonstrate the efficiency of our method and the impact on graphics and visualization techniques via the application of line-integral convolution on 2D slices as well as the extraction of streamlines of the 3D flow. We further study the benefits of our proposed lattice by applying it to the problem of simulating smoke and show that the D3bQ15 lattice yields more detail and turbulence at a reduced computational cost.     

Support vector classification of proteomic profile spectra based on feature extraction with the bi-orthogonal discrete wavelet transform

Automatic classification of high-resolution mass spectrometry data has increasing potential to support physicians in diagnosis of diseases like cancer. The proteomic data exhibit variations among different disease states. A precise and reliable classification of mass spectra is essential for a successful diagnosis and treatment. The underlying process to obtain such reliable classification results is a crucial point. In this paper such a method is explained and a corresponding semi automatic parameterization procedure is derived. Thereby a simple straightforward classification procedure to assign mass spectra to a particular disease state is derived. The method is based on an initial preprocessing stage of the whole set of spectra followed by the bi-orthogonal discrete wavelet transform (DWT) for feature extraction. The approximation coefficients calculated from the scaling function exhibit a high peak pattern matching property and feature a denoising of the spectrum. The discriminating coefficients, selected by the Kolmogorov–Smirnov test are finally used as features for training and testing a support vector machine with both a linear and a radial basis kernel. For comparison the peak areas obtained with the it ClinProt-System ¹ [33] were analyzed using the same support vector machines. The introduced approach was evaluated on clinical MALDI-MS data sets with two classes each originating from cancer studies. The cross validated error rates using the wavelet coefficients where better than those obtained from the peak areas².     

Visual comparability of 3D regular sampling and reconstruction

The Body-Centered Cubic (BCC) and Face-Centered Cubic (FCC) lattices have been analytically shown to be more efficient sampling lattices than the traditional Cartesian Cubic (CC) lattice, but there has been no estimate of their visual comparability. Two perceptual studies (each with N = 12 participants) compared the visual quality of images rendered from BCC and FCC lattices to images rendered from the CC lattice. Images were generated from two signals: the commonly used Marschner-Lobb synthetic function and a computed tomography scan of a fish tail. Observers found that BCC and FCC could produce images of comparable visual quality to CC, using 30-35 percent fewer samples. For the images used in our studies, the L(2) error metric shows high correlation with the judgement of human observers. Using the L(2) metric as a proxy, the results of the experiments appear to extend across a wide range of images and parameter choices.     

ProbExplorer: Uncertainty‐guided Exploration and Editing of Probabilistic Medical Image Segmentation

In this paper, we develop an interactive analysis and visualization tool for probabilistic segmentation results in medical imaging. We provide a systematic approach to analyze, interact and highlight regions of segmentation uncertainty. We introduce a set of visual analysis widgets integrating different approaches to analyze multivariate probabilistic field data with direct volume rendering. We demonstrate the user's ability to identify suspicious regions (e.g. tumors) and correct the misclassification results using a novel uncertainty‐based segmentation editing technique. We evaluate our system and demonstrate its usefulness in the context of static and time‐varying medical imaging datasets.     

Color invariant chroma keying and color spill neutralization for dynamic scenes and cameras

In this article we show how temporal backdrops that alternately change their color rapidly at recording rate can aid chroma keying by transforming color spill into a neutral background illumination. Since the chosen colors sum up to white, the chromatic (color) spill component is neutralized when integrating over both backdrop states. The ability to separate both states additionally allows to compute high-quality alpha mattes. Besides the neutralization of color spill, our method is invariant to foreground colors and supports applications with real-time demands. In this article, we explain different realizations of temporal backdrops and describe how keying and color spill neutralization are carried out, how artifacts resulting from rapid motion can be reduced, and how our approach can be implemented to be compatible with common real-time post-production pipelines.     

Edge aware anisotropic diffusion for 3D scalar data

In this paper we present a novel anisotropic diffusion model targeted for 3D scalar field data. Our model preserves material boundaries as well as fine tubular structures while noise is smoothed out. One of the major novelties is the use of the directional second derivative to define material boundaries instead of the gradient magnitude for thresholding. This results in a diffusion model that has much lower sensitivity to the diffusion parameter and smoothes material boundaries consistently compared to gradient magnitude based techniques. We empirically analyze the stability and convergence of the proposed diffusion and demonstrate its de-noising capabilities for both analytic and real data. We also discuss applications in the context of volume rendering.     

Modelling water dynamics with DNDC and DAISY in a soil of the North China Plain: A comparative study

The performance of the DNDC and Daisy model to simulate the water dynamics in a floodplain soil of the North China Plain was tested and compared. While the DNDC model uses a simple cascade approach, the Daisy model applies the physically based Richard's equation for simulating water movement in soil. For model testing a three years record of the soil water content from the Dong Bei Wang experimental station near Beijing was used. There, the effect of nitrogen fertilization, irrigation and straw removal on soil water and nitrogen dynamics was investigated in a three factorial field experiment applying a split-split-plot design with 4 replications. The dataset of one treatment was used for model testing and calibration. Two other independent datasets from further treatments were employed for validating the models. For both models, the simulation results were not satisfying using default parameters. After parameter optimisation and the use of site-specific van Genuchten parameters, however, the Daisy model performed well. But, for the DNDC model, parameter optimisation failed to improve the simulation result. Owing to the fact that many biological processes such as plant growth, nitrification or denitrification depend strongly on the soil water content, our findings bring us to the conclusion that the site-specific suitability of the DNDC model for simulating the soil water dynamics should be tested before further simulation of other processes.     

Constant-phase-mode operation of the light-addressable potentiometric sensor

The constant-phase-mode operation of the light-addressable potentiometric sensor (LAPS) is proposed and demonstrated. In this new operation mode, the temporal change and the spatial distribution of the analyte concentration are recorded in the form of the bias voltage applied to the LAPS sensor plate, which is servo-controlled to maintain the phase of the photocurrent at a constant value with respect to the light modulation. The constant-phase-mode LAPS is advantageous for its wider measurement range and reduction of artifacts.     

A high-density multi-point LAPS set-up using a VCSEL array and FPGA control

A new LAPS (light-addressable potentiometric sensor) set-up will be introduced, in which the light sources are miniaturised by the utilisation of a VCSEL (vertical-cavity surface-emitting laser) array to increase the measurement spot density. An FPGA (field-programmable gate array) is used to generate modulation signals for individual illumination of each measurement spot of the LAPS. The new set-up can operate a large number of measurement spots simultaneously by reading out the sum photocurrent and separate the signals of the individual measurement spots by an FFT analysis. The frequency, amplitude and offset of the modulation signal can be configured for each measurement spot by software. The new system can be combined with a positioning stage allowing the parallel read out of a single line of measurement spots and a scan perpendicular to that line in a similar manner, like for an optical scanner set-up. First measurements demonstrate the functionality of the new LAPS set-up as a chemical imaging system.