Tools for quantitative form description : an evaluation of different software packages for semi-landmark analysis

The challenging complexity of biological structures has led to the development of several methods for quantitative analyses of form. Bones are shaped by the interaction of historical (phylogenetic), structural, and functional constrains. Consequently, bone shape has been investigated intensively in an evolutionary context. Geometric morphometric approaches allow the description of the shape of an object in all of its biological complexity. However, when biological objects present only few anatomical landmarks, sliding semi-landmarks may provide good descriptors of shape. The sliding procedure, mandatory for sliding semi-landmarks, requires several steps that may be time-consuming. We here compare the time required by two different software packages ('Edgewarp' and 'Morpho') for the same sliding task, and investigate potential differences in the results and biological interpretation. 'Morpho' is much faster than 'Edgewarp,' notably as a result of the greater computational power of the 'Morpho' software routines and the complexity of the 'Edgewarp' workflow. Morphospaces obtained using both software packages are similar and provide a consistent description of the biological variability. The principal differences between the two software packages are observed in areas characterized by abrupt changes in the bone topography. In summary, both software packages perform equally well in terms of the description of biological structures, yet differ in the simplicity of the workflow and time needed to performthe analyses

The interaction of lean and building information modeling in construction

Lean construction and Building Information Modeling are quite different initiatives, but both are having profound impacts on the construction industry. A rigorous analysis of the myriad specific interactions between them indicates that a synergy exists which, if properly understood in theoretical terms, can be exploited to improve construction processes beyond the degree to which it might be improved by application of either of these paradigms independently. Using a matrix that juxtaposes BIM functionalities with prescriptive lean construction principles, fifty-six interactions have been identified, all but four of which represent constructive interaction. Although evidence for the majority of these has been found, the matrix is not considered complete, but rather a framework for research to explore the degree of validity of the interactions. Construction executives, managers, designers and developers of IT systems for construction can also benefit from the framework as an aid to recognizing the potential synergies when planning their lean and BIM adoption strategies

Hypothesis exploration with visualization of variance.

BackgroundThe Consortium for Neuropsychiatric Phenomics (CNP) at UCLA was an investigation into the biological bases of traits such as memory and response inhibition phenotypes-to explore whether they are linked to syndromes including ADHD, Bipolar disorder, and Schizophrenia. An aim of the consortium was in moving from traditional categorical approaches for psychiatric syndromes towards more quantitative approaches based on large-scale analysis of the space of human variation. It represented an application of phenomics-wide-scale, systematic study of phenotypes-to neuropsychiatry research.ResultsThis paper reports on a system for exploration of hypotheses in data obtained from the LA2K, LA3C, and LA5C studies in CNP. ViVA is a system for exploratory data analysis using novel mathematical models and methods for visualization of variance. An example of these methods is called VISOVA, a combination of visualization and analysis of variance, with the flavor of exploration associated with ANOVA in biomedical hypothesis generation. It permits visual identification of phenotype profiles-patterns of values across phenotypes-that characterize groups. Visualization enables screening and refinement of hypotheses about variance structure of sets of phenotypes.ConclusionsThe ViVA system was designed for exploration of neuropsychiatric hypotheses by interdisciplinary teams. Automated visualization in ViVA supports 'natural selection' on a pool of hypotheses, and permits deeper understanding of the statistical architecture of the data. Large-scale perspective of this kind could lead to better neuropsychiatric diagnostics

Towards cost-efficient prospection and 3D visualization of underwater structures using compact ROVs

The deployment of Remotely Operated Vehicles (ROV) for underwater prospection and 3D visualization has grown significantly in civil applications for a few decades. The demand for a wide range of optical and physical parameters of underwater environments is explained by an increasing complexity of the monitoring requirements of these environments. The prospection of engineering constructions (e.g. quay walls or enclosure doors) and underwater heritage (e.g. wrecks or sunken structures) heavily relies on ROV systems. Furthermore, ROVs offer a very flexible platform to measure the chemical content of the water. The biggest bottleneck of currently available ROVs is the cost of the systems. This constrains the availability of ROVs to a limited number of companies and institutes. Fortunately, as with the recent introduction of cost-efficient Unmanned Aerial Vehicles on the consumer market, a parallel development is expected for ROVs. The ability to participate in this new field of expertise by building Do It Yourself (DIY) kits and by adapting and adding on-demand features to the platform will increase the range of this new technology. In this paper, the construction of a DIY OpenROV kit and its implementation in bathymetric research projects are elaborated. The original platform contains a modified webcam for visual underwater prospection and a Micro ElectroMechanical System (MEMS) based depth sensor, allowing relative positioning. However, the performance of the standard camera is limited and an absolute positioning system is absent. It is expected that 3D visualizations with conventional photogrammetric qualities are limited with the current system. Therefore, modifications to improve the standard platform are foreseen, allowing the development of a cost-efficient underwater platform. Preliminary results and expectations on these challenges are reported in this paper

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

Reducing the Barrier to Entry of Complex Robotic Software: a MoveIt! Case Study

Developing robot agnostic software frameworks involves synthesizing the disparate fields of robotic theory and software engineering while simultaneously accounting for a large variability in hardware designs and control paradigms. As the capabilities of robotic software frameworks increase, the setup difficulty and learning curve for new users also increase. If the entry barriers for configuring and using the software on robots is too high, even the most powerful of frameworks are useless. A growing need exists in robotic software engineering to aid users in getting started with, and customizing, the software framework as necessary for particular robotic applications. In this paper a case study is presented for the best practices found for lowering the barrier of entry in the MoveIt! framework, an open-source tool for mobile manipulation in ROS, that allows users to 1) quickly get basic motion planning functionality with minimal initial setup, 2) automate its configuration and optimization, and 3) easily customize its components. A graphical interface that assists the user in configuring MoveIt! is the cornerstone of our approach, coupled with the use of an existing standardized robot model for input, automatically generated robot-specific configuration files, and a plugin-based architecture for extensibility. These best practices are summarized into a set of barrier to entry design principles applicable to other robotic software. The approaches for lowering the entry barrier are evaluated by usage statistics, a user survey, and compared against our design objectives for their effectiveness to users