CONFIGR: A Vision-Based Model for Long-Range Figure Completion

CONFIGR (CONtour FIgure GRound) is a computational model based on principles of biological vision that completes sparse and noisy image figures. Within an integrated vision/recognition system, CONFIGR posits an initial recognition stage which identifies figure pixels from spatially local input information. The resulting, and typically incomplete, figure is fed back to the “early vision” stage for long-range completion via filling-in. The reconstructed image is then re-presented to the recognition system for global functions such as object recognition. In the CONFIGR algorithm, the smallest independent image unit is the visible pixel, whose size defines a computational spatial scale. Once pixel size is fixed, the entire algorithm is fully determined, with no additional parameter choices. Multi-scale simulations illustrate the vision/recognition system. Open-source CONFIGR code is available online, but all examples can be derived analytically, and the design principles applied at each step are transparent. The model balances filling-in as figure against complementary filling-in as ground, which blocks spurious figure completions. Lobe computations occur on a subpixel spatial scale. Originally designed to fill-in missing contours in an incomplete image such as a dashed line, the same CONFIGR system connects and segments sparse dots, and unifies occluded objects from pieces locally identified as figure in the initial recognition stage. The model self-scales its completion distances, filling-in across gaps of any length, where unimpeded, while limiting connections among dense image-figure pixel groups that already have intrinsic form. Long-range image completion promises to play an important role in adaptive processors that reconstruct images from highly compressed video and still camera images.

KInNeSS: A Modular Framework for Computational Neuroscience

Making use of very detailed neurophysiological, anatomical, and behavioral data to build biologically-realistic computational models of animal behavior is often a difficult task. Until recently, many software packages have tried to resolve this mismatched granularity with different approaches. This paper presents KInNeSS, the KDE Integrated NeuroSimulation Software environment, as an alternative solution to bridge the gap between data and model behavior. This open source neural simulation software package provides an expandable framework incorporating features such as ease of use, scalability, an XML based schema, and multiple levels of granularity within a modern object oriented programming design. KInNeSS is best suited to simulate networks of hundreds to thousands of branched multi-compartmental neurons with biophysical properties such as membrane potential, voltage-gated and ligand-gated channels, the presence of gap junctions or ionic diffusion, neuromodulation channel gating, the mechanism for habituative or depressive synapses, axonal delays, and synaptic plasticity. KInNeSS outputs include compartment membrane voltage, spikes, local-field potentials, and current source densities, as well as visualization of the behavior of a simulated agent. An explanation of the modeling philosophy and plug-in development is also presented. Further development of KInNeSS is ongoing with the ultimate goal of creating a modular framework that will help researchers across different disciplines to effectively collaborate using a modern neural simulation platform.

Searching the Sky with CONFIGR-STARS

SyNAPSE program of the Defense Advanced Projects Research Agency (HRL Laboratories LLC, subcontract #801881-BS under DARPA prime contract HR0011-09-C-0001); CELEST, a National Science Foundation Science of Learning Center (SBE-0354378)

Design history: exploring corporate communities

A design history is a narrative involving a multitude of social groups, interpretive flexibility, and eventual stabilization of shared understanding. Design history surfaces the practices that help shape and define engagements and can increase not only our theoretical understanding of what design is, but also our capacity to realize this understanding in practice. We use a design history perspective to examine how corporate technology initiatives establish and support open source communities and the crafting of relevant design practices that enable their advancement. We foster an evolving expression of design research that treats artifacts not as stable objects to be singularly evaluated, but as evolving systems contingent on historical trajectories.

permGPU: Using graphics processing units in RNA microarray association studies.

BACKGROUND: Many analyses of microarray association studies involve permutation, bootstrap resampling and cross-validation, that are ideally formulated as embarrassingly parallel computing problems. Given that these analyses are computationally intensive, scalable approaches that can take advantage of multi-core processor systems need to be developed. RESULTS: We have developed a CUDA based implementation, permGPU, that employs graphics processing units in microarray association studies. We illustrate the performance and applicability of permGPU within the context of permutation resampling for a number of test statistics. An extensive simulation study demonstrates a dramatic increase in performance when using permGPU on an NVIDIA GTX 280 card compared to an optimized C/C++ solution running on a conventional Linux server. CONCLUSIONS: permGPU is available as an open-source stand-alone application and as an extension package for the R statistical environment. It provides a dramatic increase in performance for permutation resampling analysis in the context of microarray association studies. The current version offers six test statistics for carrying out permutation resampling analyses for binary, quantitative and censored time-to-event traits.

WormSizer: high-throughput analysis of nematode size and shape.

The fundamental phenotypes of growth rate, size and morphology are the result of complex interactions between genotype and environment. We developed a high-throughput software application, WormSizer, which computes size and shape of nematodes from brightfield images. Existing methods for estimating volume either coarsely model the nematode as a cylinder or assume the worm shape or opacity is invariant. Our estimate is more robust to changes in morphology or optical density as it only assumes radial symmetry. This open source software is written as a plugin for the well-known image-processing framework Fiji/ImageJ. It may therefore be extended easily. We evaluated the technical performance of this framework, and we used it to analyze growth and shape of several canonical Caenorhabditis elegans mutants in a developmental time series. We confirm quantitatively that a Dumpy (Dpy) mutant is short and fat and that a Long (Lon) mutant is long and thin. We show that daf-2 insulin-like receptor mutants are larger than wild-type upon hatching but grow slow, and WormSizer can distinguish dauer larvae from normal larvae. We also show that a Small (Sma) mutant is actually smaller than wild-type at all stages of larval development. WormSizer works with Uncoordinated (Unc) and Roller (Rol) mutants as well, indicating that it can be used with mutants despite behavioral phenotypes. We used our complete data set to perform a power analysis, giving users a sense of how many images are needed to detect different effect sizes. Our analysis confirms and extends on existing phenotypic characterization of well-characterized mutants, demonstrating the utility and robustness of WormSizer.

Monte Carlo Analysis and Physics Characterization of a Novel Nanoparticle Detector for Medical and Micro-dosimetry Applications

The outcomes for both (i) radiation therapy and (ii) preclinical small animal radio- biology studies are dependent on the delivery of a known quantity of radiation to a specific and intentional location. Adverse effects can result from these procedures if the dose to the target is too high or low, and can also result from an incorrect spatial distribution in which nearby normal healthy tissue can be undesirably damaged by poor radiation delivery techniques. Thus, in mice and humans alike, the spatial dose distributions from radiation sources should be well characterized in terms of the absolute dose quantity, and with pin-point accuracy. When dealing with the steep spatial dose gradients consequential to either (i) high dose rate (HDR) brachytherapy or (ii) within the small organs and tissue inhomogeneities of mice, obtaining accurate and highly precise dose results can be very challenging, considering commercially available radiation detection tools, such as ion chambers, are often too large for in-vivo use.

In this dissertation two tools are developed and applied for both clinical and preclinical radiation measurement. The first tool is a novel radiation detector for acquiring physical measurements, fabricated from an inorganic nano-crystalline scintillator that has been fixed on an optical fiber terminus. This dosimeter allows for the measurement of point doses to sub-millimeter resolution, and has the ability to be placed in-vivo in humans and small animals. Real-time data is displayed to the user to provide instant quality assurance and dose-rate information. The second tool utilizes an open source Monte Carlo particle transport code, and was applied for small animal dosimetry studies to calculate organ doses and recommend new techniques of dose prescription in mice, as well as to characterize dose to the murine bone marrow compartment with micron-scale resolution.

Hardware design changes were implemented to reduce the overall fiber diameter to <0.9 mm for the nano-crystalline scintillator based fiber optic detector (NanoFOD) system. Lower limits of device sensitivity were found to be approximately 0.05 cGy/s. Herein, this detector was demonstrated to perform quality assurance of clinical 192Ir HDR brachytherapy procedures, providing comparable dose measurements as thermo-luminescent dosimeters and accuracy within 20% of the treatment planning software (TPS) for 27 treatments conducted, with an inter-quartile range ratio to the TPS dose value of (1.02-0.94=0.08). After removing contaminant signals (Cerenkov and diode background), calibration of the detector enabled accurate dose measurements for vaginal applicator brachytherapy procedures. For 192Ir use, energy response changed by a factor of 2.25 over the SDD values of 3 to 9 cm; however a cap made of 0.2 mm thickness silver reduced energy dependence to a factor of 1.25 over the same SDD range, but had the consequence of reducing overall sensitivity by 33%.

For preclinical measurements, dose accuracy of the NanoFOD was within 1.3% of MOSFET measured dose values in a cylindrical mouse phantom at 225 kV for x-ray irradiation at angles of 0, 90, 180, and 270˝. The NanoFOD exhibited small changes in angular sensitivity, with a coefficient of variation (COV) of 3.6% at 120 kV and 1% at 225 kV. When the NanoFOD was placed alongside a MOSFET in the liver of a sacrificed mouse and treatment was delivered at 225 kV with 0.3 mm Cu filter, the dose difference was only 1.09% with use of the 4x4 cm collimator, and -0.03% with no collimation. Additionally, the NanoFOD utilized a scintillator of 11 µm thickness to measure small x-ray fields for microbeam radiation therapy (MRT) applications, and achieved 2.7% dose accuracy of the microbeam peak in comparison to radiochromic film. Modest differences between the full-width at half maximum measured lateral dimension of the MRT system were observed between the NanoFOD (420 µm) and radiochromic film (320 µm), but these differences have been explained mostly as an artifact due to the geometry used and volumetric effects in the scintillator material. Characterization of the energy dependence for the yttrium-oxide based scintillator material was performed in the range of 40-320 kV (2 mm Al filtration), and the maximum device sensitivity was achieved at 100 kV. Tissue maximum ratio data measurements were carried out on a small animal x-ray irradiator system at 320 kV and demonstrated an average difference of 0.9% as compared to a MOSFET dosimeter in the range of 2.5 to 33 cm depth in tissue equivalent plastic blocks. Irradiation of the NanoFOD fiber and scintillator material on a 137Cs gamma irradiator to 1600 Gy did not produce any measurable change in light output, suggesting that the NanoFOD system may be re-used without the need for replacement or recalibration over its lifetime.

For small animal irradiator systems, researchers can deliver a given dose to a target organ by controlling exposure time. Currently, researchers calculate this exposure time by dividing the total dose that they wish to deliver by a single provided dose rate value. This method is independent of the target organ. Studies conducted here used Monte Carlo particle transport codes to justify a new method of dose prescription in mice, that considers organ specific doses. Monte Carlo simulations were performed in the Geant4 Application for Tomographic Emission (GATE) toolkit using a MOBY mouse whole-body phantom. The non-homogeneous phantom was comprised of 256x256x800 voxels of size 0.145x0.145x0.145 mm3. Differences of up to 20-30% in dose to soft-tissue target organs was demonstrated, and methods for alleviating these errors were suggested during whole body radiation of mice by utilizing organ specific and x-ray tube filter specific dose rates for all irradiations.

Monte Carlo analysis was used on 1 µm resolution CT images of a mouse femur and a mouse vertebra to calculate the dose gradients within the bone marrow (BM) compartment of mice based on different radiation beam qualities relevant to x-ray and isotope type irradiators. Results and findings indicated that soft x-ray beams (160 kV at 0.62 mm Cu HVL and 320 kV at 1 mm Cu HVL) lead to substantially higher dose to BM within close proximity to mineral bone (within about 60 µm) as compared to hard x-ray beams (320 kV at 4 mm Cu HVL) and isotope based gamma irradiators (137Cs). The average dose increases to the BM in the vertebra for these four aforementioned radiation beam qualities were found to be 31%, 17%, 8%, and 1%, respectively. Both in-vitro and in-vivo experimental studies confirmed these simulation results, demonstrating that the 320 kV, 1 mm Cu HVL beam caused statistically significant increased killing to the BM cells at 6 Gy dose levels in comparison to both the 320 kV, 4 mm Cu HVL and the 662 keV, 137Cs beams.

Airborne transport of Saharan dust to the Mediterranean and to the Atlantic

The Sahara desert is a significant source of particulate pollution not only to the Mediterranean region, but also to the Atlantic and beyond. In this paper, PM 10 exceedences recorded in the UK and the island of Crete are studied and their source investigated, using Lagrangian Particle Dispersion (LPD) methods. Forward and inverse simulations identify Saharan dust storms as the primary source of these episodes. The methodology used allows comparison between this primary source and other possible candidates, for example large forest fires or volcanic eruptions. Two LPD models are used in the simulations, namely the open source code FLEXPART and the proprietary code HYSPLIT. Driven by the same meteorological fields (the ECMWF MARS archive and the PSU/NCAR Mesoscale model, known as MM5) the codes produce similar, but not identical predictions. This inter-model comparison enables a critical assessment of the physical modelling assumptions employed in each code, plus the influence of boundary conditions and solution grid density. The outputs, in the form of particle concentrations evolving in time, are compared against satellite images and receptor data from multiple ground-based sites. Quantitative comparisons are good, especially in predicting the time of arrival of the dust plume in a particular location.

Knowledge networks change during radical and incremental innovation episodes: a case study on software developmen

The role intra-organizational knowledge exchanges play in innovation processes has been widely acknowledged in the organizational literature. This paper contributes to the understanding of which specific configurations knowledge networks assume during different phases of radical and incremental innovation processes. The case study we selected is a FLOSS (Free/Libre Open Source Software) community consisting of 233 developers committed to the development of a web browser application since November 2002. By harvesting the mailing list, official blog and code repository of a FLOSS community, we investigate the patterns of knowledge exchange and individual contributions of its developers. We measure structural cohesion and compare global and local network properties at different points in time. Preliminary results show that phases of radical and incremental innovation are associated with specific configurations of the knowledge network as a whole as well as with different network positions of the core developers of the software.

Advanced product development integration architecture: an out-of-box solution to support distributed production networks

This paper presents novel collaboration methods implemented using a centralized client/server product development integration architecture, and a decentralized peer-to-peer network for smaller and larger companies using open source solutions. The product development integration architecture has been developed for the integration of disparate technologies and software systems for the benefit of collaborative work teams in design and manufacturing. This will facilitate the communication of early design and product development within a distributed and collaborative environment. The novelty of this work is the introduction of an‘out-of-box’ concept which provides a standard framework and deploys this utilizing a proprietary state-of-the-art product lifecycle management system (PLM). The term ‘out-of-box’ means to modify the product development and business processes to suit the technologies rather than vice versa. The key business benefits of adopting such an approach are a rapidly reconfigurable network and minimal requirements for software customization to avoid systems instability

Evaluation of the new ESR network software for the retrieval of direct sun products from cimel ce318 and prede pom01 sun-sky radiometers.

The European Skynet Radiometers network (EuroSkyRad or ESR) has been recently established as a research network of European PREDE sun-sky radiometers. Moreover, ESR is federated with SKYNET, an international network of PREDE sun-sky radiometers mostly present in East Asia. In contrast to SKYNET, the European network also integrates users of the CIMEL CE318 sky–sun photometer. Keeping instrumental duality in mind, a set of open source algorithms has been developed consisting of two modules for (1) the retrieval of direct sun products (aerosol optical depth, wavelength exponent and water vapor) from the sun extinction measurements; and (2) the inversion of the sky radiance to derive other aerosol optical properties such as size distribution, single scattering albedo or refractive index. In this study we evaluate the ESR direct sun products in comparison with the AERosol RObotic NETwork (AERONET) products. Specifically, we have applied the ESR algorithm to a CIMEL CE318 and PREDE POM simultaneously for a 4-yr database measured at the Burjassot site (Valencia, Spain), and compared the resultant products with the AERONET direct sun measurements obtained with the same CIMEL CE318 sky–sun photometer. The comparison shows that aerosol optical depth differences are mostly within the nominal uncertainty of 0.003 for a standard calibration instrument, and fall within the nominal AERONET uncertainty of 0.01–0.02 for a field instrument in the spectral range 340 to 1020 nm. In the cases of the Ångström exponent and the columnar water vapor, the differences are lower than 0.02 and 0.15 cm, respectively. Therefore, we present an open source code program that can be used with both CIMEL and PREDE sky radiometers and whose results are equivalent to AERONET and SKYNET retrievals.

A general framework for aquatic biogeochemical models

One of the most of challenging steps in the development of coupled hydrodynamic-biogeochemical models is the combination of multiple, often incompatible computer codes that describe individual physical, chemical, biological and geological processes. This “coupling” is time-consuming, error-prone, and demanding in terms of scientific and programming expertise. The open source, Fortran-based Framework for Aquatic Biogeochemical Models addresses these problems by providing a consistent set of programming interfaces through which hydrodynamic and biogeochemical models communicate. Models are coded once to connect to FABM, after which arbitrary combinations of hydrodynamic and biogeochemical models can be made. Thus, a biogeochemical model code works unmodified within models of a chemostat, a vertically structured water column, and a three-dimensional basin. Moreover, complex biogeochemistry can be distributed over many compact, self-contained modules, coupled at run-time. By enabling distributed development and user-controlled coupling of biogeochemical models, FABM enables optimal use of the expertise of scientists, programmers and end-users.

Is the General Public Licence a Rational Choice?

Open source projects are networks of developers, distributors and end-users of non-proprietary created knowledge goods. It has been argued that this form of organization has some advantages over the firm or market coordination. I show that for sufficiently convex and modular projects proprietary licences are not able to sustain sequential knowledge production which, however, can be carried out if the project is run on the open source basis.

Density Matrix Renormalization Group for Dummies

We describe the Density Matrix Renormalization Group algorithms for time dependent and time independent Hamiltonians. This paper is a brief but comprehensive introduction to the subject for anyone willing to enter in the field or write the program source code from scratch. An open source version of the code can be found at: http://www.dmrg.it.