Model-based Segmentation and Image Fusion of 3D Computed Tomography and 3D Ultrasound of the Eye for Radiotherapy Planning

For radiotherapy treatment planning of retinoblastoma inchildhood, Computed Tomography (CT) represents thestandard method for tumor volume delineation, despitesome inherent limitations. CT scan is very useful inproviding information on physical density for dosecalculation and morphological volumetric information butpresents a low sensitivity in assessing the tumorviability. On the other hand, 3D ultrasound (US) allows ahigh accurate definition of the tumor volume thanks toits high spatial resolution but it is not currentlyintegrated in the treatment planning but used only fordiagnosis and follow-up. Our ultimate goal is anautomatic segmentation of gross tumor volume (GTV) in the3D US, the segmentation of the organs at risk (OAR) inthe CT and the registration of both. In this paper, wepresent some preliminary results in this direction. Wepresent 3D active contour-based segmentation of the eyeball and the lens in CT images; the presented approachincorporates the prior knowledge of the anatomy by usinga 3D geometrical eye model. The automated segmentationresults are validated by comparing with manualsegmentations. Then, for the fusion of 3D CT and USimages, we present two approaches: (i) landmark-basedtransformation, and (ii) object-based transformation thatmakes use of eye ball contour information on CT and USimages.

Modelling hydrodynamics in the Rio Parana, Argentina : an evaluation and inter-comparison of reduced-complexity and physics based models applied to a large sand-bed river

Depth-averaged velocities and unit discharges within a 30 km reach of one of the world's largest rivers, the Rio Parana, Argentina, were simulated using three hydrodynamic models with different process representations: a reduced complexity (RC) model that neglects most of the physics governing fluid flow, a two-dimensional model based on the shallow water equations, and a three-dimensional model based on the Reynolds-averaged Navier-Stokes equations. Row characteristics simulated using all three models were compared with data obtained by acoustic Doppler current profiler surveys at four cross sections within the study reach. This analysis demonstrates that, surprisingly, the performance of the RC model is generally equal to, and in some instances better than, that of the physics based models in terms of the statistical agreement between simulated and measured flow properties. In addition, in contrast to previous applications of RC models, the present study demonstrates that the RC model can successfully predict measured flow velocities. The strong performance of the RC model reflects, in part, the simplicity of the depth-averaged mean flow patterns within the study reach and the dominant role of channel-scale topographic features in controlling the flow dynamics. Moreover, the very low water surface slopes that typify large sand-bed rivers enable flow depths to be estimated reliably in the RC model using a simple fixed-lid planar water surface approximation. This approach overcomes a major problem encountered in the application of RC models in environments characterised by shallow flows and steep bed gradients. The RC model is four orders of magnitude faster than the physics based models when performing steady-state hydrodynamic calculations. However, the iterative nature of the RC model calculations implies a reduction in computational efficiency relative to some other RC models. A further implication of this is that, if used to simulate channel morphodynamics, the present RC model may offer only a marginal advantage in terms of computational efficiency over approaches based on the shallow water equations. These observations illustrate the trade off between model realism and efficiency that is a key consideration in RC modelling. Moreover, this outcome highlights a need to rethink the use of RC morphodynamic models in fluvial geomorphology and to move away from existing grid-based approaches, such as the popular cellular automata (CA) models, that remain essentially reductionist in nature. In the case of the world's largest sand-bed rivers, this might be achieved by implementing the RC model outlined here as one element within a hierarchical modelling framework that would enable computationally efficient simulation of the morphodynamics of large rivers over millennial time scales. (C) 2012 Elsevier B.V. All rights reserved.

Efficient total variation algorithm for fetal brain MRI reconstruction.

Fetal MRI reconstruction aims at finding a high-resolution image given a small set of low-resolution images. It is usually modeled as an inverse problem where the regularization term plays a central role in the reconstruction quality. Literature has considered several regularization terms s.a. Dirichlet/Laplacian energy, Total Variation (TV)- based energies and more recently non-local means. Although TV energies are quite attractive because of their ability in edge preservation, standard explicit steepest gradient techniques have been applied to optimize fetal-based TV energies. The main contribution of this work lies in the introduction of a well-posed TV algorithm from the point of view of convex optimization. Specifically, our proposed TV optimization algorithm or fetal reconstruction is optimal w.r.t. the asymptotic and iterative convergence speeds O(1/n2) and O(1/√ε), while existing techniques are in O(1/n2) and O(1/√ε). We apply our algorithm to (1) clinical newborn data, considered as ground truth, and (2) clinical fetal acquisitions. Our algorithm compares favorably with the literature in terms of speed and accuracy.

Soil Tracking Paint Test, MLR-89-13, 1989

A new paint testing device was built to determine the resistance of paints to darkening due to road grime being tracked onto them. The device consists of a tire rotating on a sample drum. Soil was applied to the tire and then tracked onto paint samples which were attached to the drum. A colorimeter was used to measure the lightness of the paints after being tracked. Lightness is measured from 0 (absolute black) to 100 (absolute white). Four experiments were run to determine the optimum time length to track a sample, the reproducibility, the effects of different soils, and the maximum acceptable level for darkening of a paint. The following conclusions were reached: 1) the optimum tracking time was 10 minutes; 2) the reproducibility had a standard deviation of 1.5 lightness units; 3) different soils did not have a large effect on the amount of darkening on the paints; 4) a maximum acceptable darkness could not be established based on the limited amount of data; and 5) a correlation exists between the paints which were darkening in the field and the paints which were turning the darkest on the tracking wheel.

Project Newsletter Iowa Public Health Tracking, May 2014

The IDPH Public Health Tracking Program is an excellent way to collect data related to various indicators for Iowans, but those looking for national statistics or data from other states may want to check out the Health Indicators Warehouse (healthindicators.gov). Run and maintained by the CDC’s National Center for Health Statistics, this site is a centralized source for national, state, and county data for a wide variety of indicators. The data is available to the public, and can be accessed either through the tables and charts directly on the website, or indicators can be downloaded to use in a spreadsheet. Once on the site, users are able to search for their desired data either by topic or geographic region. Filters can then be applied to the chosen field to narrow down the user’s search and obtain the preferred statistics. In addition, users are also able to search for indicators derived from state and federal health indicator initiatives: County Health Rankings, Community Health Status Indicators, Healthy People 2020, and CMS Community Indicators. The warehouse provides an overview of each indicator after the user has made their selection. This overview includes information on how the data was calculated and what characteristics are being represented. For example, percent of binge drinking adults is prefaced in the overview that data was based on the question: “Considering all types of alcoholic beverages, how many times during the past 30 days did you have [5 for men, 4 for women] or more drinks on an occasion?" Data is viewable either in the basic table format, chart format, or for some indicators it is possible to view it in terms of a national map. The Health Indicators Warehouse updates indicators as data becomes available, but the collection of years varies amongst the indicators. Nonetheless, this site is a useful resource to anyone looking for comparative indicators throughout the nation or is interested in one of the hundreds of indicators housed by the site. For more information or to check out what the warehouse has to offer visit: http://healthindicators.gov/

Memory-based scheduling of scientific computing clusters

This study looks at how increased memory utilisation affects throughput and energy consumption in scientific computing, especially in high-energy physics. Our aim is to minimise energy consumed by a set of jobs without increasing the processing time. The earlier tests indicated that, especially in data analysis, throughput can increase over 100% and energy consumption decrease 50% by processing multiple jobs in parallel per CPU core. Since jobs are heterogeneous, it is not possible to find an optimum value for the number of parallel jobs. A better solution is based on memory utilisation, but finding an optimum memory threshold is not straightforward. Therefore, a fuzzy logic-based algorithm was developed that can dynamically adapt the memory threshold based on the overall load. In this way, it is possible to keep memory consumption stable with different workloads while achieving significantly higher throughput and energy-efficiency than using a traditional fixed number of jobs or fixed memory threshold approaches.

Fuzzy logic algorithm to extract specific interaction forces from atomic force microscopy data

The atomic force microscope is not only a very convenient tool for studying the topography of different samples, but it can also be used to measure specific binding forces between molecules. For this purpose, one type of molecule is attached to the tip and the other one to the substrate. Approaching the tip to the substrate allows the molecules to bind together. Retracting the tip breaks the newly formed bond. The rupture of a specific bond appears in the force-distance curves as a spike from which the binding force can be deduced. In this article we present an algorithm to automatically process force-distance curves in order to obtain bond strength histograms. The algorithm is based on a fuzzy logic approach that permits an evaluation of "quality" for every event and makes the detection procedure much faster compared to a manual selection. In this article, the software has been applied to measure the binding strength between tubuline and microtubuline associated proteins.

Comparing ICA-based and single-trial topographic ERP analyses.

Single-trial analysis of human electroencephalography (EEG) has been recently proposed for better understanding the contribution of individual subjects to a group-analysis effect as well as for investigating single-subject mechanisms. Independent Component Analysis (ICA) has been repeatedly applied to concatenated single-trial responses and at a single-subject level in order to extract those components that resemble activities of interest. More recently we have proposed a single-trial method based on topographic maps that determines which voltage configurations are reliably observed at the event-related potential (ERP) level taking advantage of repetitions across trials. Here, we investigated the correspondence between the maps obtained by ICA versus the topographies that we obtained by the single-trial clustering algorithm that best explained the variance of the ERP. To do this, we used exemplar data provided from the EEGLAB website that are based on a dataset from a visual target detection task. We show there to be robust correspondence both at the level of the activation time courses and at the level of voltage configurations of a subset of relevant maps. We additionally show the estimated inverse solution (based on low-resolution electromagnetic tomography) of two corresponding maps occurring at approximately 300 ms post-stimulus onset, as estimated by the two aforementioned approaches. The spatial distribution of the estimated sources significantly correlated and had in common a right parietal activation within Brodmann's Area (BA) 40. Despite their differences in terms of theoretical bases, the consistency between the results of these two approaches shows that their underlying assumptions are indeed compatible.

Methods for Estimating Annual Exceedance-Probability Discharges for Streams in Iowa, Based on Data through Water Year 2010, TR-519, 2013

A statewide study was performed to develop regional regression equations for estimating selected annual exceedance- probability statistics for ungaged stream sites in Iowa. The study area comprises streamgages located within Iowa and 50 miles beyond the State’s borders. Annual exceedanceprobability estimates were computed for 518 streamgages by using the expected moments algorithm to fit a Pearson Type III distribution to the logarithms of annual peak discharges for each streamgage using annual peak-discharge data through 2010. The estimation of the selected statistics included a Bayesian weighted least-squares/generalized least-squares regression analysis to update regional skew coefficients for the 518 streamgages. Low-outlier and historic information were incorporated into the annual exceedance-probability analyses, and a generalized Grubbs-Beck test was used to detect multiple potentially influential low flows. Also, geographic information system software was used to measure 59 selected basin characteristics for each streamgage. Regional regression analysis, using generalized leastsquares regression, was used to develop a set of equations for each flood region in Iowa for estimating discharges for ungaged stream sites with 50-, 20-, 10-, 4-, 2-, 1-, 0.5-, and 0.2-percent annual exceedance probabilities, which are equivalent to annual flood-frequency recurrence intervals of 2, 5, 10, 25, 50, 100, 200, and 500 years, respectively. A total of 394 streamgages were included in the development of regional regression equations for three flood regions (regions 1, 2, and 3) that were defined for Iowa based on landform regions and soil regions. Average standard errors of prediction range from 31.8 to 45.2 percent for flood region 1, 19.4 to 46.8 percent for flood region 2, and 26.5 to 43.1 percent for flood region 3. The pseudo coefficients of determination for the generalized leastsquares equations range from 90.8 to 96.2 percent for flood region 1, 91.5 to 97.9 percent for flood region 2, and 92.4 to 96.0 percent for flood region 3. The regression equations are applicable only to stream sites in Iowa with flows not significantly affected by regulation, diversion, channelization, backwater, or urbanization and with basin characteristics within the range of those used to develop the equations. These regression equations will be implemented within the U.S. Geological Survey StreamStats Web-based geographic information system tool. StreamStats allows users to click on any ungaged site on a river and compute estimates of the eight selected statistics; in addition, 90-percent prediction intervals and the measured basin characteristics for the ungaged sites also are provided by the Web-based tool. StreamStats also allows users to click on any streamgage in Iowa and estimates computed for these eight selected statistics are provided for the streamgage.

Update on the non-prewhitening model observer in computed tomography for the assessment of the adaptive statistical and model-based iterative reconstruction algorithms.

The state of the art to describe image quality in medical imaging is to assess the performance of an observer conducting a task of clinical interest. This can be done by using a model observer leading to a figure of merit such as the signal-to-noise ratio (SNR). Using the non-prewhitening (NPW) model observer, we objectively characterised the evolution of its figure of merit in various acquisition conditions. The NPW model observer usually requires the use of the modulation transfer function (MTF) as well as noise power spectra. However, although the computation of the MTF poses no problem when dealing with the traditional filtered back-projection (FBP) algorithm, this is not the case when using iterative reconstruction (IR) algorithms, such as adaptive statistical iterative reconstruction (ASIR) or model-based iterative reconstruction (MBIR). Given that the target transfer function (TTF) had already shown it could accurately express the system resolution even with non-linear algorithms, we decided to tune the NPW model observer, replacing the standard MTF by the TTF. It was estimated using a custom-made phantom containing cylindrical inserts surrounded by water. The contrast differences between the inserts and water were plotted for each acquisition condition. Then, mathematical transformations were performed leading to the TTF. As expected, the first results showed a dependency of the image contrast and noise levels on the TTF for both ASIR and MBIR. Moreover, FBP also proved to be dependent of the contrast and noise when using the lung kernel. Those results were then introduced in the NPW model observer. We observed an enhancement of SNR every time we switched from FBP to ASIR to MBIR. IR algorithms greatly improve image quality, especially in low-dose conditions. Based on our results, the use of MBIR could lead to further dose reduction in several clinical applications.

Simulated-annealing-based conditional simulation for the local-scale characterization of heterogeneous aquifers

Simulated-annealing-based conditional simulations provide a flexible means of quantitatively integrating diverse types of subsurface data. Although such techniques are being increasingly used in hydrocarbon reservoir characterization studies, their potential in environmental, engineering and hydrological investigations is still largely unexploited. Here, we introduce a novel simulated annealing (SA) algorithm geared towards the integration of high-resolution geophysical and hydrological data which, compared to more conventional approaches, provides significant advancements in the way that large-scale structural information in the geophysical data is accounted for. Model perturbations in the annealing procedure are made by drawing from a probability distribution for the target parameter conditioned to the geophysical data. This is the only place where geophysical information is utilized in our algorithm, which is in marked contrast to other approaches where model perturbations are made through the swapping of values in the simulation grid and agreement with soft data is enforced through a correlation coefficient constraint. Another major feature of our algorithm is the way in which available geostatistical information is utilized. Instead of constraining realizations to match a parametric target covariance model over a wide range of spatial lags, we constrain the realizations only at smaller lags where the available geophysical data cannot provide enough information. Thus we allow the larger-scale subsurface features resolved by the geophysical data to have much more due control on the output realizations. Further, since the only component of the SA objective function required in our approach is a covariance constraint at small lags, our method has improved convergence and computational efficiency over more traditional methods. Here, we present the results of applying our algorithm to the integration of porosity log and tomographic crosshole georadar data to generate stochastic realizations of the local-scale porosity structure. Our procedure is first tested on a synthetic data set, and then applied to data collected at the Boise Hydrogeophysical Research Site.

Comparisons of Estimates of Annual Exceedance-Probability Discharges for Small Drainage Basins in Iowa, Based on Data through Water Year 2013, TR-678, 2015

Traditionally, the Iowa Department of Transportation has used the Iowa Runoff Chart and single-variable regional-regression equations (RREs) from a U.S. Geological Survey report (published in 1987) as the primary methods to estimate annual exceedance-probability discharge (AEPD) for small (20 square miles or less) drainage basins in Iowa. With the publication of new multi- and single-variable RREs by the U.S. Geological Survey (published in 2013), the Iowa Department of Transportation needs to determine which methods of AEPD estimation provide the best accuracy and the least bias for small drainage basins in Iowa. Twenty five streamgages with drainage areas less than 2 square miles (mi2) and 55 streamgages with drainage areas between 2 and 20 mi2 were selected for the comparisons that used two evaluation metrics. Estimates of AEPDs calculated for the streamgages using the expected moments algorithm/multiple Grubbs-Beck test analysis method were compared to estimates of AEPDs calculated from the 2013 multivariable RREs; the 2013 single-variable RREs; the 1987 single-variable RREs; the TR-55 rainfall-runoff model; and the Iowa Runoff Chart. For the 25 streamgages with drainage areas less than 2 mi2, results of the comparisons seem to indicate the best overall accuracy and the least bias may be achieved by using the TR-55 method for flood regions 1 and 3 (published in 2013) and by using the 1987 single-variable RREs for flood region 2 (published in 2013). For drainage basins with areas between 2 and 20 mi2, results of the comparisons seem to indicate the best overall accuracy and the least bias may be achieved by using the 1987 single-variable RREs for the Southern Iowa Drift Plain landform region and for flood region 3 (published in 2013), by using the 2013 multivariable RREs for the Iowan Surface landform region, and by using the 2013 or 1987 single-variable RREs for flood region 2 (published in 2013). For all other landform or flood regions in Iowa, use of the 2013 single-variable RREs may provide the best overall accuracy and the least bias. An examination was conducted to understand why the 1987 single-variable RREs seem to provide better accuracy and less bias than either of the 2013 multi- or single-variable RREs. A comparison of 1-percent annual exceedance-probability regression lines for hydrologic regions 1–4 from the 1987 single-variable RREs and for flood regions 1–3 from the 2013 single-variable RREs indicates that the 1987 single-variable regional-regression lines generally have steeper slopes and lower discharges when compared to 2013 single-variable regional-regression lines for corresponding areas of Iowa. The combination of the definition of hydrologic regions, the lower discharges, and the steeper slopes of regression lines associated with the 1987 single-variable RREs seem to provide better accuracy and less bias when compared to the 2013 multi- or single-variable RREs; better accuracy and less bias was determined particularly for drainage areas less than 2 mi2, and also for some drainage areas between 2 and 20 mi2. The 2013 multi- and single-variable RREs are considered to provide better accuracy and less bias for larger drainage areas. Results of this study indicate that additional research is needed to address the curvilinear relation between drainage area and AEPDs for areas of Iowa.

Hand detection in cluttered scene images using Fourier-Mellin invariant features

This paper proposes an automatic hand detection system that combines the Fourier-Mellin Transform along with other computer vision techniques to achieve hand detection in cluttered scene color images. The proposed system uses the Fourier-Mellin Transform as an invariant feature extractor to perform RST invariant hand detection. In a first stage of the system a simple non-adaptive skin color-based image segmentation and an interest point detector based on corners are used in order to identify regions of interest that contains possible matches. A sliding window algorithm is then used to scan the image at different scales performing the FMT calculations only in the previously detected regions of interest and comparing the extracted FM descriptor of the windows with a hand descriptors database obtained from a train image set. The results of the performed experiments suggest the use of Fourier-Mellin invariant features as a promising approach for automatic hand detection.

A hybrid algorithm combining metaheuristic with Monte Carlo simulation for solving the Stochastic Flow Shop problem

In this paper, a hybrid simulation-based algorithm is proposed for the StochasticFlow Shop Problem. The main idea of the methodology is to transform the stochastic problem into a deterministic problem and then apply simulation to the latter. In order to achieve this goal, we rely on Monte Carlo Simulation and an adapted version of a deterministic heuristic. This approach aims to provide flexibility and simplicity due to the fact that it is not constrained by any previous assumption and relies in well-tested heuristics.