Tissue dynamics spectroscopy for three-dimensional tissue-based drug screening

Tissue dynamics spectroscopy combines dynamic light scattering with short-coherence digital holography to capture intracellular motion inside multicellular tumor spheroid tissue models. The cellular mechanical activity becomes an endogenous imaging contrast agent for motility contrast imaging. Fluctuation spectroscopy is performed on dynamic speckle from the proliferating shell and hypoxic core to generate drug-response spectrograms that are frequency versus time representations of the changes in spectral content induced by an applied compound or an environmental perturbation. A combination of 28 reference compounds and conditions applied to rat osteogenic UMR-106 spheroids generated spectrograms that were crosscorrelated in a similarity matrix used for unsupervised hierarchical clustering of similar compound responses. This work establishes the feasibility of tissue dynamics spectroscopy for three-dimensional tissue-based phenotypic profiling of drug response as a fully endogenous probe of the response of tissue to reference compounds.     

Picbreeder: a case study in collaborative evolutionary exploration of design space

For domains in which fitness is subjective or difficult to express formally, interactive evolutionary computation (IEC) is a natural choice. It is possible that a collaborative process combining feedback from multiple users can improve the quality and quantity of generated artifacts. Picbreeder, a large-scale online experiment in collaborative interactive evolution (CIE), explores this potential. Picbreeder is an online community in which users can evolve and share images, and most importantly, continue evolving others' images. Through this process of branching from other images, and through continually increasing image complexity made possible by the underlying neuroevolution of augmenting topologies (NEAT) algorithm, evolved images proliferate unlike in any other current IEC system. This paper discusses not only the strengths of the Picbreeder approach, but its challenges and shortcomings as well, in the hope that lessons learned will inform the design of future CIE systems.     

Measurement-based modeling of contact forces and textures for haptic rendering

Haptic texture represents the fine-grained attributes of an object's surface and is related to physical characteristics such as roughness and stiffness. We introduce an interactive and mobile scanning system for the acquisition and synthesis of haptic textures that consists of a visually tracked handheld touch probe. The most novel aspect of our work is an estimation method for the contact stiffness of an object based solely on the acceleration and forces measured during stroking of its surface with the handheld probe. We establish an experimental relationship between the estimated stiffness and the contact stiffness observed during compression. We also measure the height-displacement profile of an object's surface enabling us to generate haptic textures. We show an example of mapping the textures on to a coarse surface mesh obtained with an image-based technique, but the textures may also be combined with coarse surface meshes obtained by manual modeling.     

Shape recognition and pose estimation for mobile Augmented Reality

Nestor is a real-time recognition and camera pose estimation system for planar shapes. The system allows shapes that carry contextual meanings for humans to be used as Augmented Reality (AR) tracking targets. The user can teach the system new shapes in real time. New shapes can be shown to the system frontally, or they can be automatically rectified according to previously learned shapes. Shapes can be automatically assigned virtual content by classification according to a shape class library. Nestor performs shape recognition by analyzing contour structures and generating projective-invariant signatures from their concavities. The concavities are further used to extract features for pose estimation and tracking. Pose refinement is carried out by minimizing the reprojection error between sample points on each image contour and its library counterpart. Sample points are matched by evolving an active contour in real time. Our experiments show that the system provides stable and accurate registration, and runs at interactive frame rates on a Nokia N95 mobile phone.     

Automatic metro map layout using multicriteria optimization

This paper describes an automatic mechanism for drawing metro maps. We apply multicriteria optimization to find effective placement of stations with a good line layout and to label the map unambiguously. A number of metrics are defined, which are used in a weighted sum to find a fitness value for a layout of the map. A hill climbing optimizer is used to reduce the fitness value, and find improved map layouts. To avoid local minima, we apply clustering techniques to the map-the hill climber moves both stations and clusters when finding improved layouts. We show the method applied to a number of metro maps, and describe an empirical study that provides some quantitative evidence that automatically-drawn metro maps can help users to find routes more efficiently than either published maps or undistorted maps. Moreover, we have found that, in these cases, study subjects indicate a preference for automatically-drawn maps over the alternatives.     

Feature-based statistical analysis of combustion simulation data

We present a new framework for feature-based statistical analysis of large-scale scientific data and demonstrate its effectiveness by analyzing features from Direct Numerical Simulations (DNS) of turbulent combustion. Turbulent flows are ubiquitous and account for transport and mixing processes in combustion, astrophysics, fusion, and climate modeling among other disciplines. They are also characterized by coherent structure or organized motion, i.e. nonlocal entities whose geometrical features can directly impact molecular mixing and reactive processes. While traditional multi-point statistics provide correlative information, they lack nonlocal structural information, and hence, fail to provide mechanistic causality information between organized fluid motion and mixing and reactive processes. Hence, it is of great interest to capture and track flow features and their statistics together with their correlation with relevant scalar quantities, e.g. temperature or species concentrations. In our approach we encode the set of all possible flow features by pre-computing merge trees augmented with attributes, such as statistical moments of various scalar fields, e.g. temperature, as well as length-scales computed via spectral analysis. The computation is performed in an efficient streaming manner in a pre-processing step and results in a collection of meta-data that is orders of magnitude smaller than the original simulation data. This meta-data is sufficient to support a fully flexible and interactive analysis of the features, allowing for arbitrary thresholds, providing per-feature statistics, and creating various global diagnostics such as Cumulative Density Functions (CDFs), histograms, or time-series. We combine the analysis with a rendering of the features in a linked-view browser that enables scientists to interactively explore, visualize, and analyze the equivalent of one terabyte of simulation data. We highlight the utility of this new framework for combustion science; however, it is applicable to many other science domains.     

Nodes on ropes: a comprehensive data and control flow for steering ensemble simulations

Flood disasters are the most common natural risk and tremendous efforts are spent to improve their simulation and management. However, simulation-based investigation of actions that can be taken in case of flood emergencies is rarely done. This is in part due to the lack of a comprehensive framework which integrates and facilitates these efforts. In this paper, we tackle several problems which are related to steering a flood simulation. One issue is related to uncertainty. We need to account for uncertain knowledge about the environment, such as levee-breach locations. Furthermore, the steering process has to reveal how these uncertainties in the boundary conditions affect the confidence in the simulation outcome. Another important problem is that the simulation setup is often hidden in a black-box. We expose system internals and show that simulation steering can be comprehensible at the same time. This is important because the domain expert needs to be able to modify the simulation setup in order to include local knowledge and experience. In the proposed solution, users steer parameter studies through the World Lines interface to account for input uncertainties. The transport of steering information to the underlying data-flow components is handled by a novel meta-flow. The meta-flow is an extension to a standard data-flow network, comprising additional nodes and ropes to abstract parameter control. The meta-flow has a visual representation to inform the user about which control operations happen. Finally, we present the idea to use the data-flow diagram itself for visualizing steering information and simulation results. We discuss a case-study in collaboration with a domain expert who proposes different actions to protect a virtual city from imminent flooding. The key to choosing the best response strategy is the ability to compare different regions of the parameter space while retaining an understanding of what is happening inside the data-flow system.