Public Domain Software Research Articles

Monitoring Wnt Signaling in Zebrafish Using Fluorescent Biosensors.

In this chapter, we are presenting methods to monitor and quantify in vivo canonical Wnt signaling activities at single-cell resolution in zebrafish. Our technology is based on artificial enhancers, obtained by polymerization of TCF binding elements, cloned upstream to ubiquitous or tissue-specific promoters. The different promoter/enhancer combinations are used to drive fluorescent protein reporter constructs integrated in the zebrafish germline by microinjection of fertilized zebrafish eggs. Fish with a single integration site are selected by Mendelian analysis of fluorescent carriers, and heterozygous offspring are used to monitor and quantify canonical Wnt activities. Open source public domain software such as ImageJ/Fiji is used to calculate the integrated densities in the region of interest and compare the effect of experimental conditions on control and treated animals.

Bright-Field Imaging and Optical Coherence Tomography of the Mouse Posterior Eye.

Noninvasive live imaging has been used extensively for ocular phenotyping in mouse vision research. Bright-field imaging and optical coherence tomography (OCT) are two methods that are particularly useful for assessing the posterior mouse eye (fundus), including the retina, retinal pigment epithelium, and choroid, and are widely applied due to the commercial availability of sophisticated instruments and software. Here, we provide a guide to using these approaches with an emphasis on post-acquisition image processing using Fiji, a bundled version of the Java-based public domain software ImageJ. A bright-field fundus imaging protocol is described for acquisition of multi-frame videos, followed by image registration to reduce motion artifacts, averaging to reduce noise, shading correction to compensate for uneven illumination, filtering to improve image detail, and rotation to adjust orientation. An OCT imaging protocol is described for acquiring replicate volume scans, with subsequent registration and averaging to yield three-dimensional datasets that show reduced motion artifacts and enhanced detail. The Fiji algorithms used in these protocols are designed for batch processing and are freely available. The image acquisition and processing approaches described here may facilitate quantitative phenotyping of the mouse eye in drug discovery, mutagenesis screening, and the functional cataloging of mouse genes by individual laboratories and large-scale projects, such as the Knockout Mouse Phenotyping Project and International Mouse Phenotyping Consortium.

Open Source Software for 1D Airborne Electromagnetic Inversion

SUMMARY Geoscience Australia is releasing into the public domain software for the inversion of airborne electromagnetic (AEM) data to a 1D conductivity depth structure. The software includes two different algorithms for 1D inversion of AEM data. The first is a gradient based deterministic inversion code for multi-layer (smooth model) and few-layered (blocky-model) inversions. The second is a reversible-jump Markov chain Monte Carlo stochastic inversion algorithm suitable for assessing model uncertainty. A forward modelling program and some other ancillary programs are also included. The code is capable of inverting data from all of the commercial time-domain systems available in Australia today, including dual moment systems. The software is accessible in three forms. As C++ source code, as binary executables for 64 bit Windows® PCs, and as a service on the Virtual Geophysics Laboratory (VGL). The code is fully parallelized for execution on a high performance cluster computer system via MPI or a multi-core shared memory workstation via OpenMP.

An Optimum Wind Solar Hybrid System for Stand –Alone Power Generation

The dynamic behaviour and simulation results of a stand – alone hybrid power generation system comprising of a wind turbine, solar array and battery storage are presented in this Paper. The objective of this study is to review the state of the simulation, optimization and control technologies of the stand-alone hybrid solar–wind energy system with the inclusion of battery storage. The hybrid system used for the simulation consisted of a 100W wind turbine, 150W solar array and a 70Ah lead acid battery. A Fuzzy Logic Maximum Power Point Tracker (MPPT) controller was applied to the variable–speed, fixed–pitch small scale wind turbine while maximum power point tracking (MPPT) method based on Perturb & Observation (P&O) searching algorithm was applied to the stand–alone solar photovoltaic system. MATLAB SimulinkTM 7.2 / Simpower system software environment was utilized to accomplish and simulate individual wind and PV dynamic models of the hybrid system. The public domain software, Hybrid Optimization Model for Electric Renewables (HOMER) produced by the National Renewable Energy Laboratory was used to optimize the hybrid system with data taken from a feasibility study together with meteorological data obtained from a selected area in Sri Lanka ENGINEER, Vol. 48, No.04, pp. 1-15, 2015

Measuring Abdominal Circumference and Skeletal Muscle From a Single Cross-Sectional Computed Tomography Image: A Step-by-Step Guide for Clinicians Using National Institutes of Health ImageJ.

Diagnostic computed tomography (CT) scans provide numerous opportunities for body composition analysis, including quantification of abdominal circumference, abdominal adipose tissues (subcutaneous, visceral, and intermuscular), and skeletal muscle (SM). CT scans are commonly performed for diagnostic purposes in clinical settings, and methods for estimating abdominal circumference and whole-body SM mass from them have been reported. A supine abdominal circumference is a valid measure of waist circumference (WC). The valid correlation between a single cross-sectional CT image (slice) at third lumbar (L3) for abdominal SM and whole-body SM is also well established. Sarcopenia refers to the age-associated decreased in muscle mass and function. A single dimensional definition of sarcopenia using CT images that includes only assessment of low whole-body SM has been validated in clinical populations and significantly associated with negative outcomes. However, despite the availability and precision of SM data from CT scans and the relationship between these measurements and clinical outcomes, they have not become a routine component of clinical nutrition assessment. Lack of time, training, and expense are potential barriers that prevent clinicians from fully embracing this technique. This tutorial presents a systematic, step-by-step guide to quickly quantify abdominal circumference as a proxy for WC and SM using a cross-sectional CT image from a regional diagnostic CT scan for clinical identification of sarcopenia. Multiple software options are available, but this tutorial uses ImageJ, a free public-domain software developed by the National Institutes of Health.

Simple optical method for measuring free shrinkage

ObjectivesA simple optical method for measuring polymerization shrinkage of dental composites is compared with an established dilatometer. MethodsFive restorative composites were used to test the methods: Filtek Supreme Ultra (3M ESPE), Filtek LS (3M ESPE), Premise (Kerr), Gradia Direct (GC), and GC Kalore (GC). Uncured composites were attached to sandblasted silane-treated glass slides. The slides were placed sample side inside a mercury-filled dilatometer (ADAF). The mercury levels were recorded as the materials were light-cured through the glass-slides (40s). Mercury levels, which correlated with volumetric shrinkage, were recorded for 60min (N=6). For the optical method, uncured composite was placed on a smooth silicone platform. A pre-polymerization image was captured under a stereomicroscope, and the specimen was light-cured (40s). Post-polymerization images were captured at 2, 10, 60, and 90min (N=10). Composite outlines were traced to obtain projected surface areas (ImageJ) and volumetric shrinkage was calculated. Results were analyzed using two-way ANOVA (α=0.05) and Pearson Correlation tests. Shrinkage deformation for both methods was modeled using finite element analysis. ResultsVolumetric shrinkage at 60min ranged between 1.24% and 2.24% for dilatometer and 1.35–2.68% for optical methods. Optical method shrinkage was consistently higher than the dilatometer (P=.0001), but the ranking of the composites was the same (Pearson Correlation Coefficient 0.9997). Finite element analysis showed that lower shrinkage values of the dilatometer method could be attributed to bonding of its samples. SignificanceThe optical method using a general-purpose stereomicroscope and public-domain software is a simple and accurate alternative to measure free shrinkage.

Minimizing the sum of many rational functions

We consider the problem of globally minimizing the sum of many rational functions over a given compact semialgebraic set. The number of terms can be large (10 to 100), the degree of each term should be small (up to 10), and the number of variables can be relatively large (10 to 100) provided some kind of sparsity is present. We describe a formulation of the rational optimization problem as a generalized moment problem and its hierarchy of convex semidefinite relaxations. Under some conditions we prove that the sequence of optimal values converges to the globally optimal value. We show how public-domain software can be used to model and solve such problems. Finally, we also compare with the epigraph approach and the BARON software.

Porosity Characterization of Aluminium Castings by Using Particular Non-destructive Techniques

In this paper is presented an analysis of a comparison of particular non-destructive techniques: radiographic, ultrasonic, eddy current and pulsed infrared thermography to detect flaws in pressure die casting. Furthermore, a new way of the image segmentation method for porosity detection in aluminium pressure die casting using results from X-ray analysis and public domain software is proposed. The results of the research allowed verifying the possibility of using the aforesaid methods in controlled technological parameters of the casting process, and thus permitted confirming the quality of the manufactured castings. It was found that the radiographic method was the most preferred means for evaluating the quality of products and for optimizing the technological process for aluminium pressure casting. It permits a fast analysis of casting defects in the finished products, and when combined with the computer image analysis (the porosity segmentation algorithm as described in the article) it allows drawing conclusions regarding their causes (e.g. based on the size and shape analysis of the pores detected). The ultrasonic testing method can also be used to evaluate the quality of the casting (to detect it but without the possibility of interpreting the size or source of origin). The results obtained via this method allow for proper control of die casting parameters.

Using Photobleaching to Measure Spindle Microtubule Dynamics in Primary Cultures of Dividing Drosophila Meiotic Spermatocytes.

In dividing animal cells, a microtubule (MT)-based bipolar spindle governs chromosome movement. Current models propose that the spindle facilitates and/or generates translocating forces by regionally depolymerizing the kinetochore fibers (k-fibers) that bind each chromosome. It is unclear how conserved these sites and the resultant chromosome-moving mechanisms are between different dividing cell types because of the technical challenges of quantitatively studying MTs in many specimens. In particular, our knowledge of MT kinetics during the sperm-producing male meiotic divisions remains in its infancy. In this study, I use an easy-to-implement photobleaching-based assay for measuring spindle MT dynamics in primary cultures of meiotic spermatocytes isolated from the fruit fly Drosophila melanogaster. By use of standard scanning confocal microscopy features, fiducial marks were photobleached on fluorescent protein (FP)-tagged MTs. These were followed by time-lapse imaging during different division stages, and their displacement rates were calculated using public domain software. I find that k-fibers continually shorten at their poles during metaphase and anaphase A through the process of MT flux. Anaphase chromosome movement is complemented by Pac-Man, the shortening of the k-fiber at its chromosomal interface. Thus, Drosophila spermatocytes share the sites of spindle dynamism and mechanisms of chromosome movement with mitotic cells. The data reveal the applicability of the photobleaching assay for measuring MT dynamics in primary cultures. This approach can be readily applied to other systems.

Subject identification via ECG fiducial-based systems: Influence of the type of QT interval correction

Electrocardiography (ECG) has been recently proposed as biometric trait for identification purposes. Intra-individual variations of ECG might affect identification performance. These variations are mainly due to Heart Rate Variability (HRV). In particular, HRV causes changes in the QT intervals along the ECG waveforms. This work is aimed at analysing the influence of seven QT interval correction methods (based on population models) on the performance of ECG-fiducial-based identification systems. In addition, we have also considered the influence of training set size, classifier, classifier ensemble as well as the number of consecutive heartbeats in a majority voting scheme. The ECG signals used in this study were collected from thirty-nine subjects within the Physionet open access database. Public domain software was used for fiducial points detection. Results suggested that QT correction is indeed required to improve the performance. However, there is no clear choice among the seven explored approaches for QT correction (identification rate between 0.97 and 0.99). MultiLayer Perceptron and Support Vector Machine seemed to have better generalization capabilities, in terms of classification performance, with respect to Decision Tree-based classifiers. No such strong influence of the training-set size and the number of consecutive heartbeats has been observed on the majority voting scheme.

Computing translational diffusion and sedimentation coefficients: an evaluation of experimental data and programs.

Hydrodynamic characterisation of (bio)macromolecules is a well-established field. Observables linked to translational friction, such as the translational diffusion (Dt(0)(20,w)) and sedimentation (s(0)(20,w)) coefficients, are the most commonly used parameters. Both can be computed starting from high-resolution structures, with several methods available. We present here a comprehensive study of the performance of public-domain software, comparing the calculated Dt(0)(20,w) and s(0)(20,w) for a set of high-resolution structures (ranging in mass from 12,358 to 465,557 Da) with their critically appraised literature experimental counterparts. The methods/programs examined are AtoB, SoMo, BEST, Zeno (all implemented within the US-SOMO software suite) and HYDROPRO. Clear trends emerge: while all programs can reproduce Dt(0)(20,w) on average to within ±5% (range -8 to +7%), SoMo and AtoB slightly overestimate it (average +2 and +1%, range -2 to +7 and -4 to +5%, respectively), and BEST and HYDROPRO underestimate it slightly more (average -3 and -4%, range -7 to +2 and -8 to +2%, respectively). Similar trends are observed with s(0)(20,w), but the comparison is likely affected by the necessary inclusion of the partial specific volume in the computations. The somewhat less than ideal performances could result from the hydration treatment in BEST and HYDROPRO, and the bead overlap removal in SoMo and AtoB. Interestingly, a combination of SoMo overlapping bead models followed by Zeno computation produced better results, with a 0% average error (range -4 to +4%). Indeed, this might become the method of choice, once computational speed considerations now favouring the 5 Å-grid US-SOMO AtoB approach are overcome.

WE-D-204-07: Development of An ImageJ Plugin for Renal Function Quantification: RenalQuant

Purpose: Commercial workstations usually have their own software to calculate dynamic renal functions. However, usually they have low flexibility and subjectivity on delimiting kidney and background areas. The aim of this paper is to present a public domain software, called RenalQuant, capable to semi-automatically draw regions of interest on dynamic renal scintigraphies, extracting data and generating renal function quantification parameters. Methods: The software was developed in Java and written as an ImageJ-based plugin. The preprocessing and segmentation steps include the user’s selection of one time frame with higher activity in kidney’s region, compared with background, and low activity in the liver. Next, the chosen time frame is smoothed using a Gaussian low pass spatial filter (σ = 3) for noise reduction and better delimitation of kidneys. The maximum entropy thresholding method is used for segmentation. A background area is automatically placed below each kidney, and the user confirms if these regions are correctly segmented and positioned. Quantitative data are extracted and each renogram and relative renal function (RRF) value is calculated and displayed. Results: RenalQuant plugin was validated using retrospective 20 patients’ 99mTc-DTPA exams, and compared with results produced by commercial workstation software, referred as reference. The renograms intraclass correlation coefficients (ICC) were calculated and false-negative and false-positive RRF values were analyzed. The results showed that ICC values between RenalQuant plugin and reference software for both kidneys’ renograms were higher than 0.75, showing excellent reliability. Conclusion: Our results indicated RenalQuant plugin can be trustingly used to generate renograms, using DICOM dynamic renal scintigraphy exams as input. It is user friendly and user’s interaction occurs at a minimum level. Further studies have to investigate how to increase RRF accuracy and explore how to solve limitations in the segmentation step, mainly when background region has higher activity compared to kidneys. Financial support by CAPES

Comparison among operators for detecting and/or extracting or roads using the matlab software and the cartomorph software

Abstract. FCT / UNESP has been developing CARTOMORPH to be a public domain software which can be operated by users needing to extract and / or detect features from digital images. In this work, two methods were applied for the extraction and / or detection of the contours of the feature of interest (the highway) using a digital image containing part of a highway. One method was applied through the use of operators contained in the Mathematical Morphology toolbox, which is a private domain, SDC Information Systems, and the other was applied using the routine contained in the CARTOMORPH software. In the toolbox, the operators used were mmreadgray, responsible for opening the original image, mmhisteq, which softens the image, mmneg which can reverse the grayscale of pixels, and mmareaclose, which aims to remove image segmentation. This set of operators has resulted in a routine capable of extracting and / or detecting the contour of a road. The Blur and Minimum (Gblur) operator was used in the process using the CARTOMORPH software. This can detect the edges of objects present in the original blurred image, and transform them into an ideal edge ramp. Results from both methods were compared and the conclusion is that the blur and minimum (GBlur) operator gave a better performance. This finding indicates that the set of operators implemented in CARTOMORPH will be able to be operated by users in the field of cartography and related fields, thus enabling the use of a public domain software with efficient results.

The Role of Tissue Resection Length in the Determination of Post-Operative Eyelid Position for Muller’s Muscle-Conjunctival Resection Surgery

Purpose: To investigate the relationships between pre-operative marginal reflex distance (MRD), tissue resection length, phenylephrine response, and change in MRD with surgery for a cohort of individuals undergoing Muller’s muscle conjunctival resection (MMCR) surgery.Methods: All cases of MMCR surgery performed over a 13-year period at a single institution were screened for entry. Individuals with adequate photographic documentation and follow up were included. Patients with previous or concurrent upper eyelid, orbital or eyebrow disease of surgery were excluded. Marginal reflex distance (MRD) was calculated based on photographs utilizing public domain software. Data was plotted for inspection and appropriate statistical tests were performed.Results: During the study period 198 eyes fit criteria for analysis. A loose association between tissue resection length and change in MRD with surgery was found (r = 0.176, p < 0.05); this relationship was not significant in ANOVA analysis (p = 0.367). There was a strong association between MRD change with surgery and pre-operative MRD (r = 0.498, p < 0.01). Approximately 28% of the sample responded to 2.5% phenylephrine drop instillation with a greater than 2 mm increase in MRD. The response to phenylephrine was strongly associated with pre-operative MRD (r = −0.441, p < 0.01). A regression on change in MRD with surgery with tissue resection, phenylephrine response >2 mm and pre-operative MRD as variables revealed a model with pre-operative MRD as the only significant predictor (p < 0.01).Conclusion: Tissue resection length and phenylephrine response play small roles relative to pre-operative MRD in the determination of change in MRD with MMCR surgery.

Impact of the Dakota Aquifer on major-ion chemistry of Rock Creek discharge, eastern Nebraska, Midwest region

Examination of historical water-quality data (major cations and anions and total dissolved solids [TDS]) for Rock Creek, located in eastern Nebraska’s saline wetlands north of the Platte River, revealed that concentrations of sodium (Na), chloride (Cl), and TDS increased significantly in the downstream reach below the town of Ceresco, exceeding the U.S. Environmental Protection Agency (USEPA) secondary drinking water standards of 250 mg/L for Cl and 500 mg/L for TDS. Research into the probable source(s) of these inorganic constituents revealed that the Dakota Formation of Late Cretaceous age subcrops in the study area and typically yields water with elevated concentrations of Na, Cl, and TDS in southeastern Nebraska. This brackish to saline water upwells to the surficial aquifer and Rock Creek streambed. Additionally, the significant levels of Na and Cl correlate well with the occurrence of unique saline wetlands along Rock Creek downstream from Ceresco. Public-domain geochemical speciation software codes (Visual MINTEQ and NETPATH) were used to characterize and investigate aqueous geochemistry of Rock Creek discharge and to calculate mixing proportions of Dakota Formation water and stream discharge. The NETPATH output suggests that 3.3%–18% of discharge in Rock Creek approximately 10 km (6.2 mi) southeast of Ceresco, Nebraska, originates from the Dakota Formation and probably the underlying Pennsylvanian bedrock. Hopefully, this paper will be the impetus for an up-to-date, comprehensive, and geochemical-rich data investigation of the Dakota Aquifer’s impact on the inorganic water quality of Rock Creek.

A Bayesian approach to removal of incoherent scattering from neutron total-scattering data

A Bayesian statistics approach for subtraction of incoherent scattering from neutron total-scattering data has been developed and implemented in a public domain software package. In this approach, the estimated background signal associated with incoherent scattering maximizes the posterior probability, which combines the likelihood of this signal in reciprocal and real spaces with the prior that favors smooth lines. The probability distributions are constructed according to the principle of maximum entropy. The method enables robust subtraction of incoherent-scattering backgrounds while providing estimated uncertainties for recovered signals. The developed procedure was first tested using simulated data and then demonstrated using three representative experimental data sets, collected on bulk materials and nanoparticles, featuring distinct ratios of coherent to incoherent scattering.

Towards component-based validation of GATE: Aspects of the coincidence processor

GATE is public domain software widely used for Monte Carlo simulation in emission tomography. Validations of GATE have primarily been performed on a whole-system basis, leaving the possibility that errors in one sub-system may be offset by errors in others. We assess the accuracy of the GATE PET coincidence generation sub-system in isolation, focusing on the options most closely modeling the majority of commercially available scanners.Independent coincidence generators were coded by teams at Toshiba Medical Research Unit (TMRU) and UC Davis. A model similar to the Siemens mCT scanner was created in GATE. Annihilation photons interacting with the detectors were recorded. Coincidences were generated using GATE, TMRU and UC Davis code and results compared to “ground truth” obtained from the history of the photon interactions. GATE was tested twice, once with every qualified single event opening a time window and initiating a coincidence check (the “multiple window method”), and once where a time window is opened and a coincidence check initiated only by the first single event to occur after the end of the prior time window (the “single window method”). True, scattered and random coincidences were compared. Noise equivalent count rates were also computed and compared.The TMRU and UC Davis coincidence generators agree well with ground truth. With GATE, reasonable accuracy can be obtained if the single window method option is chosen and random coincidences are estimated without use of the delayed coincidence option. However in this GATE version, other parameter combinations can result in significant errors.

REASONING UNDER UNCERTAINTY WITH BAYESIAN BELIEF NETWORKS ENHANCED WITH ROUGH SETS

The objective of this paper is to present a new approach to reasoning under uncertainty, based on the use of Bayesian belief networks (BBN’s) enhanced with rough sets. The role of rough sets is to provide additional reasoning to assist a BBN in the inference process, in cases of missing data or difficulties with assessing the values of related probabilities. The basic concepts of both theories, BBN’s and rough sets, are briefly introduced, with examples showing how they have been traditionally used to reason under uncertainty. Two case studies from the authors’ own research are discussed: one based on the evaluation of software tool quality for use in real-time safety-critical applications, and another based on assisting the decision maker in taking the right course of action, in real time, in the naval military exercise. The use of corresponding public domain software packages based on BBN’s and rough sets is outlined, and their application for real-time reasoning in processes under uncertainty is presented.

Three-Dimensional Reconstructions From Computed Tomographic Scans on Smartphones and Tablets: A Simple Tutorial for the Ward and Operating Room Using Public Domain Software

Handling 3-dimensional reconstructions of computed tomographic scans on portable devices is problematic because of the size of the Digital Imaging and Communications in Medicine (DICOM) stacks. The authors provide a user-friendly method allowing the production, transfer, and sharing of good-quality 3-dimensional reconstructions on smartphones and tablets.

Quantitative method for in vitro matrigel invasiveness measurement through image analysis software.

The determination of cell invasion by matrigel assay is usually evaluated by counting cells able to pass through a porous membrane and attach themselves to the other side, or by an indirect quantification of eluted specific cell staining dye by means of optical density measurement. This paper describes a quantitative analytical imaging approach for determining the invasiveness of tumor cells using a simple method, based on images processing with the public domain software, ImageJ. Images obtained by direct capture are split into the red channel, and the generated image is used to measure the area that cells cover in the picture. To overcome the several disadvantages that classical cell invasion determinations present, we propose this method because it generates more accurate and sensitive determinations, and it could be a reasonable option for improving the quality of the results. The cost-effective alternative method proposed is based on this simple and robust software that is worldwide affordable.