Fault Tree Analysis Application for Safety and Reliability

NASA Technical Reports Server (NTRS)

Wallace, Dolores R.

2003-01-01

Many commercial software tools exist for fault tree analysis (FTA), an accepted method for mitigating risk in systems. The method embedded in the tools identifies a root as use in system components, but when software is identified as a root cause, it does not build trees into the software component. No commercial software tools have been built specifically for development and analysis of software fault trees. Research indicates that the methods of FTA could be applied to software, but the method is not practical without automated tool support. With appropriate automated tool support, software fault tree analysis (SFTA) may be a practical technique for identifying the underlying cause of software faults that may lead to critical system failures. We strive to demonstrate that existing commercial tools for FTA can be adapted for use with SFTA, and that applied to a safety-critical system, SFTA can be used to identify serious potential problems long before integrator and system testing.

A coverage and slicing dependencies analysis for seeking software security defects.

PubMed

He, Hui; Zhang, Dongyan; Liu, Min; Zhang, Weizhe; Gao, Dongmin

2014-01-01

Software security defects have a serious impact on the software quality and reliability. It is a major hidden danger for the operation of a system that a software system has some security flaws. When the scale of the software increases, its vulnerability has becoming much more difficult to find out. Once these vulnerabilities are exploited, it may lead to great loss. In this situation, the concept of Software Assurance is carried out by some experts. And the automated fault localization technique is a part of the research of Software Assurance. Currently, automated fault localization method includes coverage based fault localization (CBFL) and program slicing. Both of the methods have their own location advantages and defects. In this paper, we have put forward a new method, named Reverse Data Dependence Analysis Model, which integrates the two methods by analyzing the program structure. On this basis, we finally proposed a new automated fault localization method. This method not only is automation lossless but also changes the basic location unit into single sentence, which makes the location effect more accurate. Through several experiments, we proved that our method is more effective. Furthermore, we analyzed the effectiveness among these existing methods and different faults.

IFDOTMETER: A New Software Application for Automated Immunofluorescence Analysis.

PubMed

Rodríguez-Arribas, Mario; Pizarro-Estrella, Elisa; Gómez-Sánchez, Rubén; Yakhine-Diop, S M S; Gragera-Hidalgo, Antonio; Cristo, Alejandro; Bravo-San Pedro, Jose M; González-Polo, Rosa A; Fuentes, José M

2016-04-01

Most laboratories interested in autophagy use different imaging software for managing and analyzing heterogeneous parameters in immunofluorescence experiments (e.g., LC3-puncta quantification and determination of the number and size of lysosomes). One solution would be software that works on a user's laptop or workstation that can access all image settings and provide quick and easy-to-use analysis of data. Thus, we have designed and implemented an application called IFDOTMETER, which can run on all major operating systems because it has been programmed using JAVA (Sun Microsystems). Briefly, IFDOTMETER software has been created to quantify a variety of biological hallmarks, including mitochondrial morphology and nuclear condensation. The program interface is intuitive and user-friendly, making it useful for users not familiar with computer handling. By setting previously defined parameters, the software can automatically analyze a large number of images without the supervision of the researcher. Once analysis is complete, the results are stored in a spreadsheet. Using software for high-throughput cell image analysis offers researchers the possibility of performing comprehensive and precise analysis of a high number of images in an automated manner, making this routine task easier. © 2015 Society for Laboratory Automation and Screening.

Image-Based Single Cell Profiling: High-Throughput Processing of Mother Machine Experiments

PubMed Central

Sachs, Christian Carsten; Grünberger, Alexander; Helfrich, Stefan; Probst, Christopher; Wiechert, Wolfgang; Kohlheyer, Dietrich; Nöh, Katharina

2016-01-01

Background Microfluidic lab-on-chip technology combined with live-cell imaging has enabled the observation of single cells in their spatio-temporal context. The mother machine (MM) cultivation system is particularly attractive for the long-term investigation of rod-shaped bacteria since it facilitates continuous cultivation and observation of individual cells over many generations in a highly parallelized manner. To date, the lack of fully automated image analysis software limits the practical applicability of the MM as a phenotypic screening tool. Results We present an image analysis pipeline for the automated processing of MM time lapse image stacks. The pipeline supports all analysis steps, i.e., image registration, orientation correction, channel/cell detection, cell tracking, and result visualization. Tailored algorithms account for the specialized MM layout to enable a robust automated analysis. Image data generated in a two-day growth study (≈ 90 GB) is analyzed in ≈ 30 min with negligible differences in growth rate between automated and manual evaluation quality. The proposed methods are implemented in the software molyso (MOther machine AnaLYsis SOftware) that provides a new profiling tool to analyze unbiasedly hitherto inaccessible large-scale MM image stacks. Conclusion Presented is the software molyso, a ready-to-use open source software (BSD-licensed) for the unsupervised analysis of MM time-lapse image stacks. molyso source code and user manual are available at https://github.com/modsim/molyso. PMID:27661996

Using PATIMDB to Create Bacterial Transposon Insertion Mutant Libraries

PubMed Central

Urbach, Jonathan M.; Wei, Tao; Liberati, Nicole; Grenfell-Lee, Daniel; Villanueva, Jacinto; Wu, Gang; Ausubel, Frederick M.

2015-01-01

PATIMDB is a software package for facilitating the generation of transposon mutant insertion libraries. The software has two main functions: process tracking and automated sequence analysis. The process tracking function specifically includes recording the status and fates of multiwell plates and samples in various stages of library construction. Automated sequence analysis refers specifically to the pipeline of sequence analysis starting with ABI files from a sequencing facility and ending with insertion location identifications. The protocols in this unit describe installation and use of PATIMDB software. PMID:19343706

Development Status: Automation Advanced Development Space Station Freedom Electric Power System

NASA Technical Reports Server (NTRS)

Dolce, James L.; Kish, James A.; Mellor, Pamela A.

1990-01-01

Electric power system automation for Space Station Freedom is intended to operate in a loop. Data from the power system is used for diagnosis and security analysis to generate Operations Management System (OMS) requests, which are sent to an arbiter, which sends a plan to a commander generator connected to the electric power system. This viewgraph presentation profiles automation software for diagnosis, scheduling, and constraint interfaces, and simulation to support automation development. The automation development process is diagrammed, and the process of creating Ada and ART versions of the automation software is described.

PLACE: an open-source python package for laboratory automation, control, and experimentation.

PubMed

Johnson, Jami L; Tom Wörden, Henrik; van Wijk, Kasper

2015-02-01

In modern laboratories, software can drive the full experimental process from data acquisition to storage, processing, and analysis. The automation of laboratory data acquisition is an important consideration for every laboratory. When implementing a laboratory automation scheme, important parameters include its reliability, time to implement, adaptability, and compatibility with software used at other stages of experimentation. In this article, we present an open-source, flexible, and extensible Python package for Laboratory Automation, Control, and Experimentation (PLACE). The package uses modular organization and clear design principles; therefore, it can be easily customized or expanded to meet the needs of diverse laboratories. We discuss the organization of PLACE, data-handling considerations, and then present an example using PLACE for laser-ultrasound experiments. Finally, we demonstrate the seamless transition to post-processing and analysis with Python through the development of an analysis module for data produced by PLACE automation. © 2014 Society for Laboratory Automation and Screening.

Development of a fully automated software system for rapid analysis/processing of the falling weight deflectometer data.

DOT National Transportation Integrated Search

2009-02-01

The Office of Special Investigations at Iowa Department of Transportation (DOT) collects FWD data on regular basis to evaluate pavement structural conditions. The primary objective of this study was to develop a fully-automated software system for ra...

Automated data acquisition technology development:Automated modeling and control development

NASA Technical Reports Server (NTRS)

Romine, Peter L.

1995-01-01

This report documents the completion of, and improvements made to, the software developed for automated data acquisition and automated modeling and control development on the Texas Micro rackmounted PC's. This research was initiated because a need was identified by the Metal Processing Branch of NASA Marshall Space Flight Center for a mobile data acquisition and data analysis system, customized for welding measurement and calibration. Several hardware configurations were evaluated and a PC based system was chosen. The Welding Measurement System (WMS), is a dedicated instrument strickly for use of data acquisition and data analysis. In addition to the data acquisition functions described in this thesis, WMS also supports many functions associated with process control. The hardware and software requirements for an automated acquisition system for welding process parameters, welding equipment checkout, and welding process modeling were determined in 1992. From these recommendations, NASA purchased the necessary hardware and software. The new welding acquisition system is designed to collect welding parameter data and perform analysis to determine the voltage versus current arc-length relationship for VPPA welding. Once the results of this analysis are obtained, they can then be used to develop a RAIL function to control welding startup and shutdown without torch crashing.

Automated Assignment of MS/MS Cleavable Cross-Links in Protein 3D-Structure Analysis

NASA Astrophysics Data System (ADS)

Götze, Michael; Pettelkau, Jens; Fritzsche, Romy; Ihling, Christian H.; Schäfer, Mathias; Sinz, Andrea

2015-01-01

CID-MS/MS cleavable cross-linkers hold an enormous potential for an automated analysis of cross-linked products, which is essential for conducting structural proteomics studies. The created characteristic fragment ion patterns can easily be used for an automated assignment and discrimination of cross-linked products. To date, there are only a few software solutions available that make use of these properties, but none allows for an automated analysis of cleavable cross-linked products. The MeroX software fills this gap and presents a powerful tool for protein 3D-structure analysis in combination with MS/MS cleavable cross-linkers. We show that MeroX allows an automatic screening of characteristic fragment ions, considering static and variable peptide modifications, and effectively scores different types of cross-links. No manual input is required for a correct assignment of cross-links and false discovery rates are calculated. The self-explanatory graphical user interface of MeroX provides easy access for an automated cross-link search platform that is compatible with commonly used data file formats, enabling analysis of data originating from different instruments. The combination of an MS/MS cleavable cross-linker with a dedicated software tool for data analysis provides an automated workflow for 3D-structure analysis of proteins. MeroX is available at www.StavroX.com .

Assessment of Automated Analyses of Cell Migration on Flat and Nanostructured Surfaces

PubMed Central

Grădinaru, Cristian; Łopacińska, Joanna M.; Huth, Johannes; Kestler, Hans A.; Flyvbjerg, Henrik; Mølhave, Kristian

2012-01-01

Motility studies of cells often rely on computer software that analyzes time-lapse recorded movies and establishes cell trajectories fully automatically. This raises the question of reproducibility of results, since different programs could yield significantly different results of such automated analysis. The fact that the segmentation routines of such programs are often challenged by nanostructured surfaces makes the question more pertinent. Here we illustrate how it is possible to track cells on bright field microscopy images with image analysis routines implemented in an open-source cell tracking program, PACT (Program for Automated Cell Tracking). We compare the automated motility analysis of three cell tracking programs, PACT, Autozell, and TLA, using the same movies as input for all three programs. We find that different programs track overlapping, but different subsets of cells due to different segmentation methods. Unfortunately, population averages based on such different cell populations, differ significantly in some cases. Thus, results obtained with one software package are not necessarily reproducible by other software. PMID:24688640

Automated sequence analysis and editing software for HIV drug resistance testing.

PubMed

Struck, Daniel; Wallis, Carole L; Denisov, Gennady; Lambert, Christine; Servais, Jean-Yves; Viana, Raquel V; Letsoalo, Esrom; Bronze, Michelle; Aitken, Sue C; Schuurman, Rob; Stevens, Wendy; Schmit, Jean Claude; Rinke de Wit, Tobias; Perez Bercoff, Danielle

2012-05-01

Access to antiretroviral treatment in resource-limited-settings is inevitably paralleled by the emergence of HIV drug resistance. Monitoring treatment efficacy and HIV drugs resistance testing are therefore of increasing importance in resource-limited settings. Yet low-cost technologies and procedures suited to the particular context and constraints of such settings are still lacking. The ART-A (Affordable Resistance Testing for Africa) consortium brought together public and private partners to address this issue. To develop an automated sequence analysis and editing software to support high throughput automated sequencing. The ART-A Software was designed to automatically process and edit ABI chromatograms or FASTA files from HIV-1 isolates. The ART-A Software performs the basecalling, assigns quality values, aligns query sequences against a set reference, infers a consensus sequence, identifies the HIV type and subtype, translates the nucleotide sequence to amino acids and reports insertions/deletions, premature stop codons, ambiguities and mixed calls. The results can be automatically exported to Excel to identify mutations. Automated analysis was compared to manual analysis using a panel of 1624 PR-RT sequences generated in 3 different laboratories. Discrepancies between manual and automated sequence analysis were 0.69% at the nucleotide level and 0.57% at the amino acid level (668,047 AA analyzed), and discordances at major resistance mutations were recorded in 62 cases (4.83% of differences, 0.04% of all AA) for PR and 171 (6.18% of differences, 0.03% of all AA) cases for RT. The ART-A Software is a time-sparing tool for pre-analyzing HIV and viral quasispecies sequences in high throughput laboratories and highlighting positions requiring attention. Copyright © 2012 Elsevier B.V. All rights reserved.

CellSegm - a MATLAB toolbox for high-throughput 3D cell segmentation

PubMed Central

2013-01-01

The application of fluorescence microscopy in cell biology often generates a huge amount of imaging data. Automated whole cell segmentation of such data enables the detection and analysis of individual cells, where a manual delineation is often time consuming, or practically not feasible. Furthermore, compared to manual analysis, automation normally has a higher degree of reproducibility. CellSegm, the software presented in this work, is a Matlab based command line software toolbox providing an automated whole cell segmentation of images showing surface stained cells, acquired by fluorescence microscopy. It has options for both fully automated and semi-automated cell segmentation. Major algorithmic steps are: (i) smoothing, (ii) Hessian-based ridge enhancement, (iii) marker-controlled watershed segmentation, and (iv) feature-based classfication of cell candidates. Using a wide selection of image recordings and code snippets, we demonstrate that CellSegm has the ability to detect various types of surface stained cells in 3D. After detection and outlining of individual cells, the cell candidates can be subject to software based analysis, specified and programmed by the end-user, or they can be analyzed by other software tools. A segmentation of tissue samples with appropriate characteristics is also shown to be resolvable in CellSegm. The command-line interface of CellSegm facilitates scripting of the separate tools, all implemented in Matlab, offering a high degree of flexibility and tailored workflows for the end-user. The modularity and scripting capabilities of CellSegm enable automated workflows and quantitative analysis of microscopic data, suited for high-throughput image based screening. PMID:23938087

CellSegm - a MATLAB toolbox for high-throughput 3D cell segmentation.

PubMed

Hodneland, Erlend; Kögel, Tanja; Frei, Dominik Michael; Gerdes, Hans-Hermann; Lundervold, Arvid

2013-08-09

: The application of fluorescence microscopy in cell biology often generates a huge amount of imaging data. Automated whole cell segmentation of such data enables the detection and analysis of individual cells, where a manual delineation is often time consuming, or practically not feasible. Furthermore, compared to manual analysis, automation normally has a higher degree of reproducibility. CellSegm, the software presented in this work, is a Matlab based command line software toolbox providing an automated whole cell segmentation of images showing surface stained cells, acquired by fluorescence microscopy. It has options for both fully automated and semi-automated cell segmentation. Major algorithmic steps are: (i) smoothing, (ii) Hessian-based ridge enhancement, (iii) marker-controlled watershed segmentation, and (iv) feature-based classfication of cell candidates. Using a wide selection of image recordings and code snippets, we demonstrate that CellSegm has the ability to detect various types of surface stained cells in 3D. After detection and outlining of individual cells, the cell candidates can be subject to software based analysis, specified and programmed by the end-user, or they can be analyzed by other software tools. A segmentation of tissue samples with appropriate characteristics is also shown to be resolvable in CellSegm. The command-line interface of CellSegm facilitates scripting of the separate tools, all implemented in Matlab, offering a high degree of flexibility and tailored workflows for the end-user. The modularity and scripting capabilities of CellSegm enable automated workflows and quantitative analysis of microscopic data, suited for high-throughput image based screening.

Demonstration of a Safety Analysis on a Complex System

NASA Technical Reports Server (NTRS)

Leveson, Nancy; Alfaro, Liliana; Alvarado, Christine; Brown, Molly; Hunt, Earl B.; Jaffe, Matt; Joslyn, Susan; Pinnell, Denise; Reese, Jon; Samarziya, Jeffrey;

NMR-based automated protein structure determination.

PubMed

Würz, Julia M; Kazemi, Sina; Schmidt, Elena; Bagaria, Anurag; Güntert, Peter

2017-08-15

NMR spectra analysis for protein structure determination can now in many cases be performed by automated computational methods. This overview of the computational methods for NMR protein structure analysis presents recent automated methods for signal identification in multidimensional NMR spectra, sequence-specific resonance assignment, collection of conformational restraints, and structure calculation, as implemented in the CYANA software package. These algorithms are sufficiently reliable and integrated into one software package to enable the fully automated structure determination of proteins starting from NMR spectra without manual interventions or corrections at intermediate steps, with an accuracy of 1-2 Å backbone RMSD in comparison with manually solved reference structures. Copyright © 2017 Elsevier Inc. All rights reserved.

Efficient, Multi-Scale Designs Take Flight

NASA Technical Reports Server (NTRS)

2003-01-01

Engineers can solve aerospace design problems faster and more efficiently with a versatile software product that performs automated structural analysis and sizing optimization. Collier Research Corporation's HyperSizer Structural Sizing Software is a design, analysis, and documentation tool that increases productivity and standardization for a design team. Based on established aerospace structural methods for strength, stability, and stiffness, HyperSizer can be used all the way from the conceptual design to in service support. The software originated from NASA s efforts to automate its capability to perform aircraft strength analyses, structural sizing, and weight prediction and reduction. With a strategy to combine finite element analysis with an automated design procedure, NASA s Langley Research Center led the development of a software code known as ST-SIZE from 1988 to 1995. Collier Research employees were principal developers of the code along with Langley researchers. The code evolved into one that could analyze the strength and stability of stiffened panels constructed of any material, including light-weight, fiber-reinforced composites.

OpenComet: An automated tool for comet assay image analysis

PubMed Central

Gyori, Benjamin M.; Venkatachalam, Gireedhar; Thiagarajan, P.S.; Hsu, David; Clement, Marie-Veronique

2014-01-01

Reactive species such as free radicals are constantly generated in vivo and DNA is the most important target of oxidative stress. Oxidative DNA damage is used as a predictive biomarker to monitor the risk of development of many diseases. The comet assay is widely used for measuring oxidative DNA damage at a single cell level. The analysis of comet assay output images, however, poses considerable challenges. Commercial software is costly and restrictive, while free software generally requires laborious manual tagging of cells. This paper presents OpenComet, an open-source software tool providing automated analysis of comet assay images. It uses a novel and robust method for finding comets based on geometric shape attributes and segmenting the comet heads through image intensity profile analysis. Due to automation, OpenComet is more accurate, less prone to human bias, and faster than manual analysis. A live analysis functionality also allows users to analyze images captured directly from a microscope. We have validated OpenComet on both alkaline and neutral comet assay images as well as sample images from existing software packages. Our results show that OpenComet achieves high accuracy with significantly reduced analysis time. PMID:24624335

OpenComet: an automated tool for comet assay image analysis.

PubMed

Gyori, Benjamin M; Venkatachalam, Gireedhar; Thiagarajan, P S; Hsu, David; Clement, Marie-Veronique

2014-01-01

Reactive species such as free radicals are constantly generated in vivo and DNA is the most important target of oxidative stress. Oxidative DNA damage is used as a predictive biomarker to monitor the risk of development of many diseases. The comet assay is widely used for measuring oxidative DNA damage at a single cell level. The analysis of comet assay output images, however, poses considerable challenges. Commercial software is costly and restrictive, while free software generally requires laborious manual tagging of cells. This paper presents OpenComet, an open-source software tool providing automated analysis of comet assay images. It uses a novel and robust method for finding comets based on geometric shape attributes and segmenting the comet heads through image intensity profile analysis. Due to automation, OpenComet is more accurate, less prone to human bias, and faster than manual analysis. A live analysis functionality also allows users to analyze images captured directly from a microscope. We have validated OpenComet on both alkaline and neutral comet assay images as well as sample images from existing software packages. Our results show that OpenComet achieves high accuracy with significantly reduced analysis time.

The Environmental Control and Life Support System (ECLSS) advanced automation project

NASA Technical Reports Server (NTRS)

Dewberry, Brandon S.; Carnes, Ray

1990-01-01

The objective of the environmental control and life support system (ECLSS) Advanced Automation Project is to influence the design of the initial and evolutionary Space Station Freedom Program (SSFP) ECLSS toward a man-made closed environment in which minimal flight and ground manpower is needed. Another objective includes capturing ECLSS design and development knowledge future missions. Our approach has been to (1) analyze the SSFP ECLSS, (2) envision as our goal a fully automated evolutionary environmental control system - an augmentation of the baseline, and (3) document the advanced software systems, hooks, and scars which will be necessary to achieve this goal. From this analysis, prototype software is being developed, and will be tested using air and water recovery simulations and hardware subsystems. In addition, the advanced software is being designed, developed, and tested using automation software management plan and lifecycle tools. Automated knowledge acquisition, engineering, verification and testing tools are being used to develop the software. In this way, we can capture ECLSS development knowledge for future use develop more robust and complex software, provide feedback to the knowledge based system tool community, and ensure proper visibility of our efforts.

Fully automated corneal endothelial morphometry of images captured by clinical specular microscopy

NASA Astrophysics Data System (ADS)

Bucht, Curry; Söderberg, Per; Manneberg, Göran

2010-02-01

The corneal endothelium serves as the posterior barrier of the cornea. Factors such as clarity and refractive properties of the cornea are in direct relationship to the quality of the endothelium. The endothelial cell density is considered the most important morphological factor of the corneal endothelium. Pathological conditions and physical trauma may threaten the endothelial cell density to such an extent that the optical property of the cornea and thus clear eyesight is threatened. Diagnosis of the corneal endothelium through morphometry is an important part of several clinical applications. Morphometry of the corneal endothelium is presently carried out by semi automated analysis of pictures captured by a Clinical Specular Microscope (CSM). Because of the occasional need of operator involvement, this process can be tedious, having a negative impact on sampling size. This study was dedicated to the development and use of fully automated analysis of a very large range of images of the corneal endothelium, captured by CSM, using Fourier analysis. Software was developed in the mathematical programming language Matlab. Pictures of the corneal endothelium, captured by CSM, were read into the analysis software. The software automatically performed digital enhancement of the images, normalizing lights and contrasts. The digitally enhanced images of the corneal endothelium were Fourier transformed, using the fast Fourier transform (FFT) and stored as new images. Tools were developed and applied for identification and analysis of relevant characteristics of the Fourier transformed images. The data obtained from each Fourier transformed image was used to calculate the mean cell density of its corresponding corneal endothelium. The calculation was based on well known diffraction theory. Results in form of estimated cell density of the corneal endothelium were obtained, using fully automated analysis software on 292 images captured by CSM. The cell density obtained by the fully automated analysis was compared to the cell density obtained from classical, semi-automated analysis and a relatively large correlation was found.

FloWave.US: validated, open-source, and flexible software for ultrasound blood flow analysis.

PubMed

Coolbaugh, Crystal L; Bush, Emily C; Caskey, Charles F; Damon, Bruce M; Towse, Theodore F

2016-10-01

Automated software improves the accuracy and reliability of blood velocity, vessel diameter, blood flow, and shear rate ultrasound measurements, but existing software offers limited flexibility to customize and validate analyses. We developed FloWave.US-open-source software to automate ultrasound blood flow analysis-and demonstrated the validity of its blood velocity (aggregate relative error, 4.32%) and vessel diameter (0.31%) measures with a skeletal muscle ultrasound flow phantom. Compared with a commercial, manual analysis software program, FloWave.US produced equivalent in vivo cardiac cycle time-averaged mean (TAMean) velocities at rest and following a 10-s muscle contraction (mean bias <1 pixel for both conditions). Automated analysis of ultrasound blood flow data was 9.8 times faster than the manual method. Finally, a case study of a lower extremity muscle contraction experiment highlighted the ability of FloWave.US to measure small fluctuations in TAMean velocity, vessel diameter, and mean blood flow at specific time points in the cardiac cycle. In summary, the collective features of our newly designed software-accuracy, reliability, reduced processing time, cost-effectiveness, and flexibility-offer advantages over existing proprietary options. Further, public distribution of FloWave.US allows researchers to easily access and customize code to adapt ultrasound blood flow analysis to a variety of vascular physiology applications. Copyright © 2016 the American Physiological Society.

Automated Slide Scanning and Segmentation in Fluorescently-labeled Tissues Using a Widefield High-content Analysis System.

PubMed

Poon, Candice C; Ebacher, Vincent; Liu, Katherine; Yong, Voon Wee; Kelly, John James Patrick

2018-05-03

Automated slide scanning and segmentation of fluorescently-labeled tissues is the most efficient way to analyze whole slides or large tissue sections. Unfortunately, many researchers spend large amounts of time and resources developing and optimizing workflows that are only relevant to their own experiments. In this article, we describe a protocol that can be used by those with access to a widefield high-content analysis system (WHCAS) to image any slide-mounted tissue, with options for customization within pre-built modules found in the associated software. Not originally intended for slide scanning, the steps detailed in this article make it possible to acquire slide scanning images in the WHCAS which can be imported into the associated software. In this example, the automated segmentation of brain tumor slides is demonstrated, but the automated segmentation of any fluorescently-labeled nuclear or cytoplasmic marker is possible. Furthermore, there are a variety of other quantitative software modules including assays for protein localization/translocation, cellular proliferation/viability/apoptosis, and angiogenesis that can be run. This technique will save researchers time and effort and create an automated protocol for slide analysis.

STAMPS: Software Tool for Automated MRI Post-processing on a supercomputer.

PubMed

Bigler, Don C; Aksu, Yaman; Miller, David J; Yang, Qing X

2009-08-01

This paper describes a Software Tool for Automated MRI Post-processing (STAMP) of multiple types of brain MRIs on a workstation and for parallel processing on a supercomputer (STAMPS). This software tool enables the automation of nonlinear registration for a large image set and for multiple MR image types. The tool uses standard brain MRI post-processing tools (such as SPM, FSL, and HAMMER) for multiple MR image types in a pipeline fashion. It also contains novel MRI post-processing features. The STAMP image outputs can be used to perform brain analysis using Statistical Parametric Mapping (SPM) or single-/multi-image modality brain analysis using Support Vector Machines (SVMs). Since STAMPS is PBS-based, the supercomputer may be a multi-node computer cluster or one of the latest multi-core computers.

j5 DNA assembly design automation.

PubMed

Hillson, Nathan J

2014-01-01

Modern standardized methodologies, described in detail in the previous chapters of this book, have enabled the software-automated design of optimized DNA construction protocols. This chapter describes how to design (combinatorial) scar-less DNA assembly protocols using the web-based software j5. j5 assists biomedical and biotechnological researchers construct DNA by automating the design of optimized protocols for flanking homology sequence as well as type IIS endonuclease-mediated DNA assembly methodologies. Unlike any other software tool available today, j5 designs scar-less combinatorial DNA assembly protocols, performs a cost-benefit analysis to identify which portions of an assembly process would be less expensive to outsource to a DNA synthesis service provider, and designs hierarchical DNA assembly strategies to mitigate anticipated poor assembly junction sequence performance. Software integrated with j5 add significant value to the j5 design process through graphical user-interface enhancement and downstream liquid-handling robotic laboratory automation.

Application of Artificial Intelligence technology to the analysis and synthesis of reliable software systems

NASA Technical Reports Server (NTRS)

Wild, Christian; Eckhardt, Dave

1987-01-01

The development of a methodology for the production of highly reliable software is one of the greatest challenges facing the computer industry. Meeting this challenge will undoubtably involve the integration of many technologies. This paper describes the use of Artificial Intelligence technologies in the automated analysis of the formal algebraic specifications of abstract data types. These technologies include symbolic execution of specifications using techniques of automated deduction and machine learning through the use of examples. On-going research into the role of knowledge representation and problem solving in the process of developing software is also discussed.

Dexterity: A MATLAB-based analysis software suite for processing and visualizing data from tasks that measure arm or forelimb function.

PubMed

Butensky, Samuel D; Sloan, Andrew P; Meyers, Eric; Carmel, Jason B

2017-07-15

Hand function is critical for independence, and neurological injury often impairs dexterity. To measure hand function in people or forelimb function in animals, sensors are employed to quantify manipulation. These sensors make assessment easier and more quantitative and allow automation of these tasks. While automated tasks improve objectivity and throughput, they also produce large amounts of data that can be burdensome to analyze. We created software called Dexterity that simplifies data analysis of automated reaching tasks. Dexterity is MATLAB software that enables quick analysis of data from forelimb tasks. Through a graphical user interface, files are loaded and data are identified and analyzed. These data can be annotated or graphed directly. Analysis is saved, and the graph and corresponding data can be exported. For additional analysis, Dexterity provides access to custom scripts created by other users. To determine the utility of Dexterity, we performed a study to evaluate the effects of task difficulty on the degree of impairment after injury. Dexterity analyzed two months of data and allowed new users to annotate the experiment, visualize results, and save and export data easily. Previous analysis of tasks was performed with custom data analysis, requiring expertise with analysis software. Dexterity made the tools required to analyze, visualize and annotate data easy to use by investigators without data science experience. Dexterity increases accessibility to automated tasks that measure dexterity by making analysis of large data intuitive, robust, and efficient. Copyright © 2017 Elsevier B.V. All rights reserved.

The contaminant analysis automation robot implementation for the automated laboratory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Younkin, J.R.; Igou, R.E.; Urenda, T.D.

1995-12-31

The Contaminant Analysis Automation (CAA) project defines the automated laboratory as a series of standard laboratory modules (SLM) serviced by a robotic standard support module (SSM). These SLMs are designed to allow plug-and-play integration into automated systems that perform standard analysis methods (SAM). While the SLMs are autonomous in the execution of their particular chemical processing task, the SAM concept relies on a high-level task sequence controller (TSC) to coordinate the robotic delivery of materials requisite for SLM operations, initiate an SLM operation with the chemical method dependent operating parameters, and coordinate the robotic removal of materials from the SLMmore » when its commands and events has been established to allow ready them for transport operations as well as performing the Supervisor and Subsystems (GENISAS) software governs events from the SLMs and robot. The Intelligent System Operating Environment (ISOE) enables the inter-process communications used by GENISAS. CAA selected the Hewlett-Packard Optimized Robot for Chemical Analysis (ORCA) and its associated Windows based Methods Development Software (MDS) as the robot SSM. The MDS software is used to teach the robot each SLM position and required material port motions. To allow the TSC to command these SLM motions, a hardware and software implementation was required that allowed message passing between different operating systems. This implementation involved the use of a Virtual Memory Extended (VME) rack with a Force CPU-30 computer running VxWorks; a real-time multitasking operating system, and a Radiuses PC compatible VME computer running MDS. A GENISAS server on The Force computer accepts a transport command from the TSC, a GENISAS supervisor, over Ethernet and notifies software on the RadiSys PC of the pending command through VMEbus shared memory. The command is then delivered to the MDS robot control software using a Windows Dynamic Data Exchange conversation.« less

The Stability and Validity of Automated Vocal Analysis in Preverbal Preschoolers With Autism Spectrum Disorder

PubMed Central

Woynaroski, Tiffany; Oller, D. Kimbrough; Keceli-Kaysili, Bahar; Xu, Dongxin; Richards, Jeffrey A.; Gilkerson, Jill; Gray, Sharmistha; Yoder, Paul

2017-01-01

Theory and research suggest that vocal development predicts “useful speech” in preschoolers with autism spectrum disorder (ASD), but conventional methods for measurement of vocal development are costly and time consuming. This longitudinal correlational study examines the reliability and validity of several automated indices of vocalization development relative to an index derived from human coded, conventional communication samples in a sample of preverbal preschoolers with ASD. Automated indices of vocal development were derived using software that is presently “in development” and/or only available for research purposes and using commercially available Language ENvironment Analysis (LENA) software. Indices of vocal development that could be derived using the software available for research purposes: (a) were highly stable with a single day-long audio recording, (b) predicted future spoken vocabulary to a degree that was nonsignificantly different from the index derived from conventional communication samples, and (c) continued to predict future spoken vocabulary even after controlling for concurrent vocabulary in our sample. The score derived from standard LENA software was similarly stable, but was not significantly correlated with future spoken vocabulary. Findings suggest that automated vocal analysis is a valid and reliable alternative to time intensive and expensive conventional communication samples for measurement of vocal development of preverbal preschoolers with ASD in research and clinical practice. PMID:27459107

Automated Sensitivity Analysis of Interplanetary Trajectories

NASA Technical Reports Server (NTRS)

Knittel, Jeremy; Hughes, Kyle; Englander, Jacob; Sarli, Bruno

2017-01-01

This work describes a suite of Python tools known as the Python EMTG Automated Trade Study Application (PEATSA). PEATSA was written to automate the operation of trajectory optimization software, simplify the process of performing sensitivity analysis, and was ultimately found to out-perform a human trajectory designer in unexpected ways. These benefits will be discussed and demonstrated on sample mission designs.

Software Construction and Analysis Tools for Future Space Missions

NASA Technical Reports Server (NTRS)

Lowry, Michael R.; Clancy, Daniel (Technical Monitor)

2002-01-01

NASA and its international partners will increasingly depend on software-based systems to implement advanced functions for future space missions, such as Martian rovers that autonomously navigate long distances exploring geographic features formed by surface water early in the planet's history. The software-based functions for these missions will need to be robust and highly reliable, raising significant challenges in the context of recent Mars mission failures attributed to software faults. After reviewing these challenges, this paper describes tools that have been developed at NASA Ames that could contribute to meeting these challenges; 1) Program synthesis tools based on automated inference that generate documentation for manual review and annotations for automated certification. 2) Model-checking tools for concurrent object-oriented software that achieve memorability through synergy with program abstraction and static analysis tools.

Design and implementation of software for automated quality control and data analysis for a complex LC/MS/MS assay for urine opiates and metabolites.

PubMed

Dickerson, Jane A; Schmeling, Michael; Hoofnagle, Andrew N; Hoffman, Noah G

2013-01-16

Mass spectrometry provides a powerful platform for performing quantitative, multiplexed assays in the clinical laboratory, but at the cost of increased complexity of analysis and quality assurance calculations compared to other methodologies. Here we describe the design and implementation of a software application that performs quality control calculations for a complex, multiplexed, mass spectrometric analysis of opioids and opioid metabolites. The development and implementation of this application improved our data analysis and quality assurance processes in several ways. First, use of the software significantly improved the procedural consistency for performing quality control calculations. Second, it reduced the amount of time technologists spent preparing and reviewing the data, saving on average over four hours per run, and in some cases improving turnaround time by a day. Third, it provides a mechanism for coupling procedural and software changes with the results of each analysis. We describe several key details of the implementation including the use of version control software and automated unit tests. These generally useful software engineering principles should be considered for any software development project in the clinical lab. Copyright © 2012 Elsevier B.V. All rights reserved.

Automatic sample changer control software for automation of neutron activation analysis process in Malaysian Nuclear Agency

NASA Astrophysics Data System (ADS)

Yussup, N.; Ibrahim, M. M.; Rahman, N. A. A.; Mokhtar, M.; Salim, N. A. A.; Soh@Shaari, S. C.; Azman, A.; Lombigit, L.; Azman, A.; Omar, S. A.

2018-01-01

Most of the procedures in neutron activation analysis (NAA) process that has been established in Malaysian Nuclear Agency (Nuclear Malaysia) since 1980s were performed manually. These manual procedures carried out by the NAA laboratory personnel are time consuming and inefficient especially for sample counting and measurement process. The sample needs to be changed and the measurement software needs to be setup for every one hour counting time. Both of these procedures are performed manually for every sample. Hence, an automatic sample changer system (ASC) that consists of hardware and software is developed to automate sample counting process for up to 30 samples consecutively. This paper describes the ASC control software for NAA process which is designed and developed to control the ASC hardware and call GammaVision software for sample measurement. The software is developed by using National Instrument LabVIEW development package.

Automated Sensitivity Analysis of Interplanetary Trajectories for Optimal Mission Design

NASA Technical Reports Server (NTRS)

Knittel, Jeremy; Hughes, Kyle; Englander, Jacob; Sarli, Bruno

2017-01-01

This work describes a suite of Python tools known as the Python EMTG Automated Trade Study Application (PEATSA). PEATSA was written to automate the operation of trajectory optimization software, simplify the process of performing sensitivity analysis, and was ultimately found to out-perform a human trajectory designer in unexpected ways. These benefits will be discussed and demonstrated on sample mission designs.

Automated quantification of neuronal networks and single-cell calcium dynamics using calcium imaging

PubMed Central

Patel, Tapan P.; Man, Karen; Firestein, Bonnie L.; Meaney, David F.

2017-01-01

Background Recent advances in genetically engineered calcium and membrane potential indicators provide the potential to estimate the activation dynamics of individual neurons within larger, mesoscale networks (100s–1000 +neurons). However, a fully integrated automated workflow for the analysis and visualization of neural microcircuits from high speed fluorescence imaging data is lacking. New method Here we introduce FluoroSNNAP, Fluorescence Single Neuron and Network Analysis Package. FluoroSNNAP is an open-source, interactive software developed in MATLAB for automated quantification of numerous biologically relevant features of both the calcium dynamics of single-cells and network activity patterns. FluoroSNNAP integrates and improves upon existing tools for spike detection, synchronization analysis, and inference of functional connectivity, making it most useful to experimentalists with little or no programming knowledge. Results We apply FluoroSNNAP to characterize the activity patterns of neuronal microcircuits undergoing developmental maturation in vitro. Separately, we highlight the utility of single-cell analysis for phenotyping a mixed population of neurons expressing a human mutant variant of the microtubule associated protein tau and wild-type tau. Comparison with existing method(s) We show the performance of semi-automated cell segmentation using spatiotemporal independent component analysis and significant improvement in detecting calcium transients using a template-based algorithm in comparison to peak-based or wavelet-based detection methods. Our software further enables automated analysis of microcircuits, which is an improvement over existing methods. Conclusions We expect the dissemination of this software will facilitate a comprehensive analysis of neuronal networks, promoting the rapid interrogation of circuits in health and disease. PMID:25629800

A LabVIEW®-based software for the control of the AUTORAD platform: a fully automated multisequential flow injection analysis Lab-on-Valve (MSFIA-LOV) system for radiochemical analysis.

PubMed

Barbesi, Donato; Vicente Vilas, Víctor; Millet, Sylvain; Sandow, Miguel; Colle, Jean-Yves; Aldave de Las Heras, Laura

2017-01-01

A LabVIEW ® -based software for the control of the fully automated multi-sequential flow injection analysis Lab-on-Valve (MSFIA-LOV) platform AutoRAD performing radiochemical analysis is described. The analytical platform interfaces an Arduino ® -based device triggering multiple detectors providing a flexible and fit for purpose choice of detection systems. The different analytical devices are interfaced to the PC running LabVIEW ® VI software using USB and RS232 interfaces, both for sending commands and receiving confirmation or error responses. The AUTORAD platform has been successfully applied for the chemical separation and determination of Sr, an important fission product pertinent to nuclear waste.

The Holistic Targeting (HOT) Methodology as the Means to Improve Information Operations (IO) Target Development and Prioritization

DTIC Science & Technology

2008-09-01

software facilitate targeting problem understanding and the network analysis tool, Palantir , as an efficient and tailored semi-automated means to...the use of compendium software facilitate targeting problem understanding and the network analysis tool, Palantir , as an efficient and tailored semi...OBJECTIVES USING COMPENDIUM SOFTWARE .....63 E. HOT TARGET PRIORITIZATION AND DEVELOPMENT USING PALANTIR SOFTWARE .................................69 1

Quantitative analysis of cardiovascular MR images.

PubMed

van der Geest, R J; de Roos, A; van der Wall, E E; Reiber, J H

1997-06-01

The diagnosis of cardiovascular disease requires the precise assessment of both morphology and function. Nearly all aspects of cardiovascular function and flow can be quantified nowadays with fast magnetic resonance (MR) imaging techniques. Conventional and breath-hold cine MR imaging allow the precise and highly reproducible assessment of global and regional left ventricular function. During the same examination, velocity encoded cine (VEC) MR imaging provides measurements of blood flow in the heart and great vessels. Quantitative image analysis often still relies on manual tracing of contours in the images. Reliable automated or semi-automated image analysis software would be very helpful to overcome the limitations associated with the manual and tedious processing of the images. Recent progress in MR imaging of the coronary arteries and myocardial perfusion imaging with contrast media, along with the further development of faster imaging sequences, suggest that MR imaging could evolve into a single technique ('one stop shop') for the evaluation of many aspects of heart disease. As a result, it is very likely that the need for automated image segmentation and analysis software algorithms will further increase. In this paper the developments directed towards the automated image analysis and semi-automated contour detection for cardiovascular MR imaging are presented.

A methodology for producing reliable software, volume 1

NASA Technical Reports Server (NTRS)

Stucki, L. G.; Moranda, P. B.; Foshee, G.; Kirchoff, M.; Omre, R.

1976-01-01

An investigation into the areas having an impact on producing reliable software including automated verification tools, software modeling, testing techniques, structured programming, and management techniques is presented. This final report contains the results of this investigation, analysis of each technique, and the definition of a methodology for producing reliable software.

Semi-automated and automated glioma grading using dynamic susceptibility-weighted contrast-enhanced perfusion MRI relative cerebral blood volume measurements.

PubMed

Friedman, S N; Bambrough, P J; Kotsarini, C; Khandanpour, N; Hoggard, N

2012-12-01

Despite the established role of MRI in the diagnosis of brain tumours, histopathological assessment remains the clinically used technique, especially for the glioma group. Relative cerebral blood volume (rCBV) is a dynamic susceptibility-weighted contrast-enhanced perfusion MRI parameter that has been shown to correlate to tumour grade, but assessment requires a specialist and is time consuming. We developed analysis software to determine glioma gradings from perfusion rCBV scans in a manner that is quick, easy and does not require a specialist operator. MRI perfusion data from 47 patients with different histopathological grades of glioma were analysed with custom-designed software. Semi-automated analysis was performed with a specialist and non-specialist operator separately determining the maximum rCBV value corresponding to the tumour. Automated histogram analysis was performed by calculating the mean, standard deviation, median, mode, skewness and kurtosis of rCBV values. All values were compared with the histopathologically assessed tumour grade. A strong correlation between specialist and non-specialist observer measurements was found. Significantly different values were obtained between tumour grades using both semi-automated and automated techniques, consistent with previous results. The raw (unnormalised) data single-pixel maximum rCBV semi-automated analysis value had the strongest correlation with glioma grade. Standard deviation of the raw data had the strongest correlation of the automated analysis. Semi-automated calculation of raw maximum rCBV value was the best indicator of tumour grade and does not require a specialist operator. Both semi-automated and automated MRI perfusion techniques provide viable non-invasive alternatives to biopsy for glioma tumour grading.

Identification of genes in anonymous DNA sequences. Annual performance report, February 1, 1991--January 31, 1992

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fields, C.A.

1996-06-01

The objective of this project is the development of practical software to automate the identification of genes in anonymous DNA sequences from the human, and other higher eukaryotic genomes. A software system for automated sequence analysis, gm (gene modeler) has been designed, implemented, tested, and distributed to several dozen laboratories worldwide. A significantly faster, more robust, and more flexible version of this software, gm 2.0 has now been completed, and is being tested by operational use to analyze human cosmid sequence data. A range of efforts to further understand the features of eukaryoyic gene sequences are also underway. This progressmore » report also contains papers coming out of the project including the following: gm: a Tool for Exploratory Analysis of DNA Sequence Data; The Human THE-LTR(O) and MstII Interspersed Repeats are subfamilies of a single widely distruted highly variable repeat family; Information contents and dinucleotide compostions of plant intron sequences vary with evolutionary origin; Splicing signals in Drosophila: intron size, information content, and consensus sequences; Integration of automated sequence analysis into mapping and sequencing projects; Software for the C. elegans genome project.« less

Clarity: An Open Source Manager for Laboratory Automation

PubMed Central

Delaney, Nigel F.; Echenique, José Rojas; Marx, Christopher J.

2013-01-01

Software to manage automated laboratories interfaces with hardware instruments, gives users a way to specify experimental protocols, and schedules activities to avoid hardware conflicts. In addition to these basics, modern laboratories need software that can run multiple different protocols in parallel and that can be easily extended to interface with a constantly growing diversity of techniques and instruments. We present Clarity: a laboratory automation manager that is hardware agnostic, portable, extensible and open source. Clarity provides critical features including remote monitoring, robust error reporting by phone or email, and full state recovery in the event of a system crash. We discuss the basic organization of Clarity; demonstrate an example of its implementation for the automated analysis of bacterial growth; and describe how the program can be extended to manage new hardware. Clarity is mature; well documented; actively developed; written in C# for the Common Language Infrastructure; and is free and open source software. These advantages set Clarity apart from currently available laboratory automation programs. PMID:23032169

The Imagery of Sound

NASA Technical Reports Server (NTRS)

2000-01-01

Automated Analysis Corporation's COMET is a suite of acoustic analysis software for advanced noise prediction. It analyzes the origin, radiation, and scattering of noise, and supplies information on how to achieve noise reduction and improve sound characteristics. COMET's Structural Acoustic Foam Engineering (SAFE) module extends the sound field analysis capability of foam and other materials. SAFE shows how noise travels while airborne, how it travels within a structure, and how these media interact to affect other aspects of the transmission of noise. The COMET software reduces design time and expense while optimizing a final product's acoustical performance. COMET was developed through SBIR funding and Langley Research Center for Automated Analysis Corporation.

A digital flight control system verification laboratory

NASA Technical Reports Server (NTRS)

De Feo, P.; Saib, S.

1982-01-01

A NASA/FAA program has been established for the verification and validation of digital flight control systems (DFCS), with the primary objective being the development and analysis of automated verification tools. In order to enhance the capabilities, effectiveness, and ease of using the test environment, software verification tools can be applied. Tool design includes a static analyzer, an assertion generator, a symbolic executor, a dynamic analysis instrument, and an automated documentation generator. Static and dynamic tools are integrated with error detection capabilities, resulting in a facility which analyzes a representative testbed of DFCS software. Future investigations will ensue particularly in the areas of increase in the number of software test tools, and a cost effectiveness assessment.

Pilot Study of an Open-source Image Analysis Software for Automated Screening of Conventional Cervical Smears.

PubMed

Sanyal, Parikshit; Ganguli, Prosenjit; Barui, Sanghita; Deb, Prabal

2018-01-01

The Pap stained cervical smear is a screening tool for cervical cancer. Commercial systems are used for automated screening of liquid based cervical smears. However, there is no image analysis software used for conventional cervical smears. The aim of this study was to develop and test the diagnostic accuracy of a software for analysis of conventional smears. The software was developed using Python programming language and open source libraries. It was standardized with images from Bethesda Interobserver Reproducibility Project. One hundred and thirty images from smears which were reported Negative for Intraepithelial Lesion or Malignancy (NILM), and 45 images where some abnormality has been reported, were collected from the archives of the hospital. The software was then tested on the images. The software was able to segregate images based on overall nuclear: cytoplasmic ratio, coefficient of variation (CV) in nuclear size, nuclear membrane irregularity, and clustering. 68.88% of abnormal images were flagged by the software, as well as 19.23% of NILM images. The major difficulties faced were segmentation of overlapping cell clusters and separation of neutrophils. The software shows potential as a screening tool for conventional cervical smears; however, further refinement in technique is required.

New Results in Software Model Checking and Analysis

NASA Technical Reports Server (NTRS)

Pasareanu, Corina S.

2010-01-01

This introductory article surveys new techniques, supported by automated tools, for the analysis of software to ensure reliability and safety. Special focus is on model checking techniques. The article also introduces the five papers that are enclosed in this special journal volume.

Validity of automated measurement of left ventricular ejection fraction and volume using the Philips EPIQ system.

PubMed

Hovnanians, Ninel; Win, Theresa; Makkiya, Mohammed; Zheng, Qi; Taub, Cynthia

2017-11-01

To assess the efficiency and reproducibility of automated measurements of left ventricular (LV) volumes and LV ejection fraction (LVEF) in comparison to manually traced biplane Simpson's method. This is a single-center prospective study. Apical four- and two-chamber views were acquired in patients in sinus rhythm. Two operators independently measured LV volumes and LVEF using biplane Simpson's method. In addition, the image analysis software a2DQ on the Philips EPIQ system was applied to automatically assess the LV volumes and LVEF. Time spent on each analysis, using both methods, was documented. Concordance of echocardiographic measures was evaluated using intraclass correlation (ICC) and Bland-Altman analysis. Manual tracing and automated measurement of LV volumes and LVEF were performed in 184 patients with a mean age of 67.3 ± 17.3 years and BMI 28.0 ± 6.8 kg/m 2 . ICC and Bland-Altman analysis showed good agreements between manual and automated methods measuring LVEF, end-systolic, and end-diastolic volumes. The average analysis time was significantly less using the automated method than manual tracing (116 vs 217 seconds/patient, P < .0001). Automated measurement using the novel image analysis software a2DQ on the Philips EPIQ system produced accurate, efficient, and reproducible assessment of LV volumes and LVEF compared with manual measurement. © 2017, Wiley Periodicals, Inc.

Intelligent software for laboratory automation.

PubMed

Whelan, Ken E; King, Ross D

2004-09-01

The automation of laboratory techniques has greatly increased the number of experiments that can be carried out in the chemical and biological sciences. Until recently, this automation has focused primarily on improving hardware. Here we argue that future advances will concentrate on intelligent software to integrate physical experimentation and results analysis with hypothesis formulation and experiment planning. To illustrate our thesis, we describe the 'Robot Scientist' - the first physically implemented example of such a closed loop system. In the Robot Scientist, experimentation is performed by a laboratory robot, hypotheses concerning the results are generated by machine learning and experiments are allocated and selected by a combination of techniques derived from artificial intelligence research. The performance of the Robot Scientist has been evaluated by a rediscovery task based on yeast functional genomics. The Robot Scientist is proof that the integration of programmable laboratory hardware and intelligent software can be used to develop increasingly automated laboratories.

Sample registration software for process automation in the Neutron Activation Analysis (NAA) Facility in Malaysia nuclear agency

NASA Astrophysics Data System (ADS)

Rahman, Nur Aira Abd; Yussup, Nolida; Salim, Nazaratul Ashifa Bt. Abdullah; Ibrahim, Maslina Bt. Mohd; Mokhtar, Mukhlis B.; Soh@Shaari, Syirrazie Bin Che; Azman, Azraf B.; Ismail, Nadiah Binti

2015-04-01

Neutron Activation Analysis (NAA) had been established in Nuclear Malaysia since 1980s. Most of the procedures established were done manually including sample registration. The samples were recorded manually in a logbook and given ID number. Then all samples, standards, SRM and blank were recorded on the irradiation vial and several forms prior to irradiation. These manual procedures carried out by the NAA laboratory personnel were time consuming and not efficient. Sample registration software is developed as part of IAEA/CRP project on `Development of Process Automation in the Neutron Activation Analysis (NAA) Facility in Malaysia Nuclear Agency (RC17399)'. The objective of the project is to create a pc-based data entry software during sample preparation stage. This is an effective method to replace redundant manual data entries that needs to be completed by laboratory personnel. The software developed will automatically generate sample code for each sample in one batch, create printable registration forms for administration purpose, and store selected parameters that will be passed to sample analysis program. The software is developed by using National Instruments Labview 8.6.

Automating Structural Analysis of Spacecraft Vehicles

NASA Technical Reports Server (NTRS)

Hrinda, Glenn A.

2004-01-01

A major effort within NASA's vehicle analysis discipline has been to automate structural analysis and sizing optimization during conceptual design studies of advanced spacecraft. Traditional spacecraft structural sizing has involved detailed finite element analysis (FEA) requiring large degree-of-freedom (DOF) finite element models (FEM). Creation and analysis of these models can be time consuming and limit model size during conceptual designs. The goal is to find an optimal design that meets the mission requirements but produces the lightest structure. A structural sizing tool called HyperSizer has been successfully used in the conceptual design phase of a reusable launch vehicle and planetary exploration spacecraft. The program couples with FEA to enable system level performance assessments and weight predictions including design optimization of material selections and sizing of spacecraft members. The software's analysis capabilities are based on established aerospace structural methods for strength, stability and stiffness that produce adequately sized members and reliable structural weight estimates. The software also helps to identify potential structural deficiencies early in the conceptual design so changes can be made without wasted time. HyperSizer's automated analysis and sizing optimization increases productivity and brings standardization to a systems study. These benefits will be illustrated in examining two different types of conceptual spacecraft designed using the software. A hypersonic air breathing, single stage to orbit (SSTO), reusable launch vehicle (RLV) will be highlighted as well as an aeroshell for a planetary exploration vehicle used for aerocapture at Mars. By showing the two different types of vehicles, the software's flexibility will be demonstrated with an emphasis on reducing aeroshell structural weight. Member sizes, concepts and material selections will be discussed as well as analysis methods used in optimizing the structure. Analysis based on the HyperSizer structural sizing software will be discussed. Design trades required to optimize structural weight will be presented.

Automation of the Environmental Control and Life Support System

NASA Technical Reports Server (NTRS)

Dewberry, Brandon S.; Carnes, J. Ray

1990-01-01

The objective of the Environmental Control and Life Support System (ECLSS) Advanced Automation Project is to recommend and develop advanced software for the initial and evolutionary Space Station Freedom (SSF) ECLS system which will minimize the crew and ground manpower needed for operations. Another objective includes capturing ECLSS design and development knowledge for future missions. This report summarizes our results from Phase I, the ECLSS domain analysis phase, which we broke down into three steps: 1) Analyze and document the baselined ECLS system, 2) envision as our goal an evolution to a fully automated regenerative life support system, built upon an augmented baseline, and 3) document the augmentations (hooks and scars) and advanced software systems which we see as necessary in achieving minimal manpower support for ECLSS operations. In addition, Phase I included development of an advanced software life cycle testing tools will be used in the development of the software. In this way, we plan in preparation for phase II and III, the development and integration phases, respectively. Automated knowledge acquisition, engineering, verification, and can capture ECLSS development knowledge for future use, develop more robust and complex software, provide feedback to the KBS tool community, and insure proper visibility of our efforts.

Automated measurement of zebrafish larval movement

PubMed Central

Cario, Clinton L; Farrell, Thomas C; Milanese, Chiara; Burton, Edward A

2011-01-01

Abstract The zebrafish is a powerful vertebrate model that is readily amenable to genetic, pharmacological and environmental manipulations to elucidate the molecular and cellular basis of movement and behaviour. We report software enabling automated analysis of zebrafish movement from video recordings captured with cameras ranging from a basic camcorder to more specialized equipment. The software, which is provided as open-source MATLAB functions, can be freely modified and distributed, and is compatible with multiwell plates under a wide range of experimental conditions. Automated measurement of zebrafish movement using this technique will be useful for multiple applications in neuroscience, pharmacology and neuropsychiatry. PMID:21646414

Automated measurement of zebrafish larval movement.

PubMed

Cario, Clinton L; Farrell, Thomas C; Milanese, Chiara; Burton, Edward A

2011-08-01

The zebrafish is a powerful vertebrate model that is readily amenable to genetic, pharmacological and environmental manipulations to elucidate the molecular and cellular basis of movement and behaviour. We report software enabling automated analysis of zebrafish movement from video recordings captured with cameras ranging from a basic camcorder to more specialized equipment. The software, which is provided as open-source MATLAB functions, can be freely modified and distributed, and is compatible with multiwell plates under a wide range of experimental conditions. Automated measurement of zebrafish movement using this technique will be useful for multiple applications in neuroscience, pharmacology and neuropsychiatry.

Will the future of knowledge work automation transform personalized medicine?

PubMed

Naik, Gauri; Bhide, Sanika S

2014-09-01

Today, we live in a world of 'information overload' which demands high level of knowledge-based work. However, advances in computer hardware and software have opened possibilities to automate 'routine cognitive tasks' for knowledge processing. Engineering intelligent software systems that can process large data sets using unstructured commands and subtle judgments and have the ability to learn 'on the fly' are a significant step towards automation of knowledge work. The applications of this technology for high throughput genomic analysis, database updating, reporting clinically significant variants, and diagnostic imaging purposes are explored using case studies.

A Novel Automated Method for Analyzing Cylindrical Computed Tomography Data

NASA Technical Reports Server (NTRS)

Roth, D. J.; Burke, E. R.; Rauser, R. W.; Martin, R. E.

2011-01-01

A novel software method is presented that is applicable for analyzing cylindrical and partially cylindrical objects inspected using computed tomography. This method involves unwrapping and re-slicing data so that the CT data from the cylindrical object can be viewed as a series of 2-D sheets in the vertical direction in addition to volume rendering and normal plane views provided by traditional CT software. The method is based on interior and exterior surface edge detection and under proper conditions, is FULLY AUTOMATED and requires no input from the user except the correct voxel dimension from the CT scan. The software is available from NASA in 32- and 64-bit versions that can be applied to gigabyte-sized data sets, processing data either in random access memory or primarily on the computer hard drive. Please inquire with the presenting author if further interested. This software differentiates itself in total from other possible re-slicing software solutions due to complete automation and advanced processing and analysis capabilities.

The stability and validity of automated vocal analysis in preverbal preschoolers with autism spectrum disorder.

PubMed

Woynaroski, Tiffany; Oller, D Kimbrough; Keceli-Kaysili, Bahar; Xu, Dongxin; Richards, Jeffrey A; Gilkerson, Jill; Gray, Sharmistha; Yoder, Paul

2017-03-01

Theory and research suggest that vocal development predicts "useful speech" in preschoolers with autism spectrum disorder (ASD), but conventional methods for measurement of vocal development are costly and time consuming. This longitudinal correlational study examines the reliability and validity of several automated indices of vocalization development relative to an index derived from human coded, conventional communication samples in a sample of preverbal preschoolers with ASD. Automated indices of vocal development were derived using software that is presently "in development" and/or only available for research purposes and using commercially available Language ENvironment Analysis (LENA) software. Indices of vocal development that could be derived using the software available for research purposes: (a) were highly stable with a single day-long audio recording, (b) predicted future spoken vocabulary to a degree that was nonsignificantly different from the index derived from conventional communication samples, and (c) continued to predict future spoken vocabulary even after controlling for concurrent vocabulary in our sample. The score derived from standard LENA software was similarly stable, but was not significantly correlated with future spoken vocabulary. Findings suggest that automated vocal analysis is a valid and reliable alternative to time intensive and expensive conventional communication samples for measurement of vocal development of preverbal preschoolers with ASD in research and clinical practice. Autism Res 2017, 10: 508-519. © 2016 International Society for Autism Research, Wiley Periodicals, Inc. © 2016 International Society for Autism Research, Wiley Periodicals, Inc.

ADP Analysis project for the Human Resources Management Division

NASA Technical Reports Server (NTRS)

Tureman, Robert L., Jr.

1993-01-01

The ADP (Automated Data Processing) Analysis Project was conducted for the Human Resources Management Division (HRMD) of NASA's Langley Research Center. The three major areas of work in the project were computer support, automated inventory analysis, and an ADP study for the Division. The goal of the computer support work was to determine automation needs of Division personnel and help them solve computing problems. The goal of automated inventory analysis was to find a way to analyze installed software and usage on a Macintosh. Finally, the ADP functional systems study for the Division was designed to assess future HRMD needs concerning ADP organization and activities.

Isothermal Titration Calorimetry Can Provide Critical Thinking Opportunities

ERIC Educational Resources Information Center

Moore, Dale E.; Goode, David R.; Seney, Caryn S.; Boatwright, Jennifer M.

2016-01-01

College chemistry faculties might not have considered including isothermal titration calorimetry (ITC) in their majors' curriculum because experimental data from this instrumental method are often analyzed via automation (software). However, the software-based data analysis can be replaced with a spreadsheet-based analysis that is readily…

Process and information integration via hypermedia

NASA Technical Reports Server (NTRS)

Hammen, David G.; Labasse, Daniel L.; Myers, Robert M.

1990-01-01

Success stories for advanced automation prototypes abound in the literature but the deployments of practical large systems are few in number. There are several factors that militate against the maturation of such prototypes into products. Here, the integration of advanced automation software into large systems is discussed. Advanced automation systems tend to be specific applications that need to be integrated and aggregated into larger systems. Systems integration can be achieved by providing expert user-developers with verified tools to efficiently create small systems that interface to large systems through standard interfaces. The use of hypermedia as such a tool in the context of the ground control centers that support Shuttle and space station operations is explored. Hypermedia can be an integrating platform for data, conventional software, and advanced automation software, enabling data integration through the display of diverse types of information and through the creation of associative links between chunks of information. Further, hypermedia enables process integration through graphical invoking of system functions. Through analysis and examples, researchers illustrate how diverse information and processing paradigms can be integrated into a single software platform.

SAGA: A project to automate the management of software production systems

NASA Technical Reports Server (NTRS)

Campbell, Roy H.; Laliberte, D.; Render, H.; Sum, R.; Smith, W.; Terwilliger, R.

1987-01-01

The Software Automation, Generation and Administration (SAGA) project is investigating the design and construction of practical software engineering environments for developing and maintaining aerospace systems and applications software. The research includes the practical organization of the software lifecycle, configuration management, software requirements specifications, executable specifications, design methodologies, programming, verification, validation and testing, version control, maintenance, the reuse of software, software libraries, documentation, and automated management.

Advanced Automation for Ion Trap Mass Spectrometry-New Opportunities for Real-Time Autonomous Analysis

NASA Technical Reports Server (NTRS)

Palmer, Peter T.; Wong, C. M.; Salmonson, J. D.; Yost, R. A.; Griffin, T. P.; Yates, N. A.; Lawless, James G. (Technical Monitor)

1994-01-01

The utility of MS/MS for both target compound analysis and the structure elucidation of unknowns has been described in a number of references. A broader acceptance of this technique has not yet been realized as it requires large, complex, and costly instrumentation which has not been competitive with more conventional techniques. Recent advancements in ion trap mass spectrometry promise to change this situation. Although the ion trap's small size, sensitivity, and ability to perform multiple stages of mass spectrometry have made it eminently suitable for on-line, real-time monitoring applications, advance automation techniques are required to make these capabilities more accessible to non-experts. Towards this end we have developed custom software for the design and implementation of MS/MS experiments. This software allows the user to take full advantage of the ion trap's versatility with respect to ionization techniques, scan proxies, and ion accumulation/ejection methods. Additionally, expert system software has been developed for autonomous target compound analysis. This software has been linked to ion trap control software and a commercial data system to bring all of the steps in the analysis cycle under control of the expert system. These software development efforts and their utilization for a number of trace analysis applications will be described.

A novel method for automated tracking and quantification of adult zebrafish behaviour during anxiety.

PubMed

Nema, Shubham; Hasan, Whidul; Bhargava, Anamika; Bhargava, Yogesh

2016-09-15

Behavioural neuroscience relies on software driven methods for behavioural assessment, but the field lacks cost-effective, robust, open source software for behavioural analysis. Here we propose a novel method which we called as ZebraTrack. It includes cost-effective imaging setup for distraction-free behavioural acquisition, automated tracking using open-source ImageJ software and workflow for extraction of behavioural endpoints. Our ImageJ algorithm is capable of providing control to users at key steps while maintaining automation in tracking without the need for the installation of external plugins. We have validated this method by testing novelty induced anxiety behaviour in adult zebrafish. Our results, in agreement with established findings, showed that during state-anxiety, zebrafish showed reduced distance travelled, increased thigmotaxis and freezing events. Furthermore, we proposed a method to represent both spatial and temporal distribution of choice-based behaviour which is currently not possible to represent using simple videograms. ZebraTrack method is simple and economical, yet robust enough to give results comparable with those obtained from costly proprietary software like Ethovision XT. We have developed and validated a novel cost-effective method for behavioural analysis of adult zebrafish using open-source ImageJ software. Copyright © 2016 Elsevier B.V. All rights reserved.

Using Automation to Improve the Flight Software Testing Process

NASA Technical Reports Server (NTRS)

ODonnell, James R., Jr.; Andrews, Stephen F.; Morgenstern, Wendy M.; Bartholomew, Maureen O.; McComas, David C.; Bauer, Frank H. (Technical Monitor)

2001-01-01

One of the critical phases in the development of a spacecraft attitude control system (ACS) is the testing of its flight software. The testing (and test verification) of ACS flight software requires a mix of skills involving software, attitude control, data manipulation, and analysis. The process of analyzing and verifying flight software test results often creates a bottleneck which dictates the speed at which flight software verification can be conducted. In the development of the Microwave Anisotropy Probe (MAP) spacecraft ACS subsystem, an integrated design environment was used that included a MAP high fidelity (HiFi) simulation, a central database of spacecraft parameters, a script language for numeric and string processing, and plotting capability. In this integrated environment, it was possible to automate many of the steps involved in flight software testing, making the entire process more efficient and thorough than on previous missions. In this paper, we will compare the testing process used on MAP to that used on previous missions. The software tools that were developed to automate testing and test verification will be discussed, including the ability to import and process test data, synchronize test data and automatically generate HiFi script files used for test verification, and an automated capability for generating comparison plots. A summary of the perceived benefits of applying these test methods on MAP will be given. Finally, the paper will conclude with a discussion of re-use of the tools and techniques presented, and the ongoing effort to apply them to flight software testing of the Triana spacecraft ACS subsystem.

Using Automation to Improve the Flight Software Testing Process

NASA Technical Reports Server (NTRS)

ODonnell, James R., Jr.; Morgenstern, Wendy M.; Bartholomew, Maureen O.

2001-01-01

One of the critical phases in the development of a spacecraft attitude control system (ACS) is the testing of its flight software. The testing (and test verification) of ACS flight software requires a mix of skills involving software, knowledge of attitude control, and attitude control hardware, data manipulation, and analysis. The process of analyzing and verifying flight software test results often creates a bottleneck which dictates the speed at which flight software verification can be conducted. In the development of the Microwave Anisotropy Probe (MAP) spacecraft ACS subsystem, an integrated design environment was used that included a MAP high fidelity (HiFi) simulation, a central database of spacecraft parameters, a script language for numeric and string processing, and plotting capability. In this integrated environment, it was possible to automate many of the steps involved in flight software testing, making the entire process more efficient and thorough than on previous missions. In this paper, we will compare the testing process used on MAP to that used on other missions. The software tools that were developed to automate testing and test verification will be discussed, including the ability to import and process test data, synchronize test data and automatically generate HiFi script files used for test verification, and an automated capability for generating comparison plots. A summary of the benefits of applying these test methods on MAP will be given. Finally, the paper will conclude with a discussion of re-use of the tools and techniques presented, and the ongoing effort to apply them to flight software testing of the Triana spacecraft ACS subsystem.

The environmental control and life support system advanced automation project. Phase 1: Application evaluation

NASA Technical Reports Server (NTRS)

Dewberry, Brandon S.

1990-01-01

The Environmental Control and Life Support System (ECLSS) is a Freedom Station distributed system with inherent applicability to advanced automation primarily due to the comparatively large reaction times of its subsystem processes. This allows longer contemplation times in which to form a more intelligent control strategy and to detect or prevent faults. The objective of the ECLSS Advanced Automation Project is to reduce the flight and ground manpower needed to support the initial and evolutionary ECLS system. The approach is to search out and make apparent those processes in the baseline system which are in need of more automatic control and fault detection strategies, to influence the ECLSS design by suggesting software hooks and hardware scars which will allow easy adaptation to advanced algorithms, and to develop complex software prototypes which fit into the ECLSS software architecture and will be shown in an ECLSS hardware testbed to increase the autonomy of the system. Covered here are the preliminary investigation and evaluation process, aimed at searching the ECLSS for candidate functions for automation and providing a software hooks and hardware scars analysis. This analysis shows changes needed in the baselined system for easy accommodation of knowledge-based or other complex implementations which, when integrated in flight or ground sustaining engineering architectures, will produce a more autonomous and fault tolerant Environmental Control and Life Support System.

Multiplex Quantitative Histologic Analysis of Human Breast Cancer Cell Signaling and Cell Fate

DTIC Science & Technology

2010-05-01

Breast cancer, cell signaling, cell proliferation, histology, image analysis 15. NUMBER OF PAGES - 51 16. PRICE CODE 17. SECURITY CLASSIFICATION...revealed by individual stains in multiplex combinations; and (3) software (FARSIGHT) for automated multispectral image analysis that (i) segments...Task 3. Develop computational algorithms for multispectral immunohistological image analysis FARSIGHT software was developed to quantify intrinsic

Automated, Parametric Geometry Modeling and Grid Generation for Turbomachinery Applications

NASA Technical Reports Server (NTRS)

Harrand, Vincent J.; Uchitel, Vadim G.; Whitmire, John B.

2000-01-01

The objective of this Phase I project is to develop a highly automated software system for rapid geometry modeling and grid generation for turbomachinery applications. The proposed system features a graphical user interface for interactive control, a direct interface to commercial CAD/PDM systems, support for IGES geometry output, and a scripting capability for obtaining a high level of automation and end-user customization of the tool. The developed system is fully parametric and highly automated, and, therefore, significantly reduces the turnaround time for 3D geometry modeling, grid generation and model setup. This facilitates design environments in which a large number of cases need to be generated, such as for parametric analysis and design optimization of turbomachinery equipment. In Phase I we have successfully demonstrated the feasibility of the approach. The system has been tested on a wide variety of turbomachinery geometries, including several impellers and a multi stage rotor-stator combination. In Phase II, we plan to integrate the developed system with turbomachinery design software and with commercial CAD/PDM software.

metAlignID: a high-throughput software tool set for automated detection of trace level contaminants in comprehensive LECO two-dimensional gas chromatography time-of-flight mass spectrometry data.

PubMed

Lommen, Arjen; van der Kamp, Henk J; Kools, Harrie J; van der Lee, Martijn K; van der Weg, Guido; Mol, Hans G J

2012-11-09

A new alternative data processing tool set, metAlignID, is developed for automated pre-processing and library-based identification and concentration estimation of target compounds after analysis by comprehensive two-dimensional gas chromatography with mass spectrometric detection. The tool set has been developed for and tested on LECO data. The software is developed to run multi-threaded (one thread per processor core) on a standard PC (personal computer) under different operating systems and is as such capable of processing multiple data sets simultaneously. Raw data files are converted into netCDF (network Common Data Form) format using a fast conversion tool. They are then preprocessed using previously developed algorithms originating from metAlign software. Next, the resulting reduced data files are searched against a user-composed library (derived from user or commercial NIST-compatible libraries) (NIST=National Institute of Standards and Technology) and the identified compounds, including an indicative concentration, are reported in Excel format. Data can be processed batch wise. The overall time needed for conversion together with processing and searching of 30 raw data sets for 560 compounds is routinely within an hour. The screening performance is evaluated for detection of pesticides and contaminants in raw data obtained after analysis of soil and plant samples. Results are compared to the existing data-handling routine based on proprietary software (LECO, ChromaTOF). The developed software tool set, which is freely downloadable at www.metalign.nl, greatly accelerates data-analysis and offers more options for fine-tuning automated identification toward specific application needs. The quality of the results obtained is slightly better than the standard processing and also adds a quantitative estimate. The software tool set in combination with two-dimensional gas chromatography coupled to time-of-flight mass spectrometry shows great potential as a highly-automated and fast multi-residue instrumental screening method. Copyright © 2012 Elsevier B.V. All rights reserved.

Sample registration software for process automation in the Neutron Activation Analysis (NAA) Facility in Malaysia nuclear agency

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rahman, Nur Aira Abd, E-mail: nur-aira@nuclearmalaysia.gov.my; Yussup, Nolida; Ibrahim, Maslina Bt. Mohd

Neutron Activation Analysis (NAA) had been established in Nuclear Malaysia since 1980s. Most of the procedures established were done manually including sample registration. The samples were recorded manually in a logbook and given ID number. Then all samples, standards, SRM and blank were recorded on the irradiation vial and several forms prior to irradiation. These manual procedures carried out by the NAA laboratory personnel were time consuming and not efficient. Sample registration software is developed as part of IAEA/CRP project on ‘Development of Process Automation in the Neutron Activation Analysis (NAA) Facility in Malaysia Nuclear Agency (RC17399)’. The objective ofmore » the project is to create a pc-based data entry software during sample preparation stage. This is an effective method to replace redundant manual data entries that needs to be completed by laboratory personnel. The software developed will automatically generate sample code for each sample in one batch, create printable registration forms for administration purpose, and store selected parameters that will be passed to sample analysis program. The software is developed by using National Instruments Labview 8.6.« less

Integrating automated structured analysis and design with Ada programming support environments

NASA Technical Reports Server (NTRS)

Hecht, Alan; Simmons, Andy

1986-01-01

Ada Programming Support Environments (APSE) include many powerful tools that address the implementation of Ada code. These tools do not address the entire software development process. Structured analysis is a methodology that addresses the creation of complete and accurate system specifications. Structured design takes a specification and derives a plan to decompose the system subcomponents, and provides heuristics to optimize the software design to minimize errors and maintenance. It can also produce the creation of useable modules. Studies have shown that most software errors result from poor system specifications, and that these errors also become more expensive to fix as the development process continues. Structured analysis and design help to uncover error in the early stages of development. The APSE tools help to insure that the code produced is correct, and aid in finding obscure coding errors. However, they do not have the capability to detect errors in specifications or to detect poor designs. An automated system for structured analysis and design TEAMWORK, which can be integrated with an APSE to support software systems development from specification through implementation is described. These tools completement each other to help developers improve quality and productivity, as well as to reduce development and maintenance costs. Complete system documentation and reusable code also resultss from the use of these tools. Integrating an APSE with automated tools for structured analysis and design provide capabilities and advantages beyond those realized with any of these systems used by themselves.

The integration of automated knowledge acquisition with computer-aided software engineering for space shuttle expert systems

NASA Technical Reports Server (NTRS)

Modesitt, Kenneth L.

1990-01-01

A prediction was made that the terms expert systems and knowledge acquisition would begin to disappear over the next several years. This is not because they are falling into disuse; it is rather that practitioners are realizing that they are valuable adjuncts to software engineering, in terms of problem domains addressed, user acceptance, and in development methodologies. A specific problem was discussed, that of constructing an automated test analysis system for the Space Shuttle Main Engine. In this domain, knowledge acquisition was part of requirements systems analysis, and was performed with the aid of a powerful inductive ESBT in conjunction with a computer aided software engineering (CASE) tool. The original prediction is not a very risky one -- it has already been accomplished.

Automated Scoring of Chromogenic Media for Detection of Methicillin-Resistant Staphylococcus aureus by Use of WASPLab Image Analysis Software.

PubMed

Faron, Matthew L; Buchan, Blake W; Vismara, Chiara; Lacchini, Carla; Bielli, Alessandra; Gesu, Giovanni; Liebregts, Theo; van Bree, Anita; Jansz, Arjan; Soucy, Genevieve; Korver, John; Ledeboer, Nathan A

2016-03-01

Recently, systems have been developed to create total laboratory automation for clinical microbiology. These systems allow for the automation of specimen processing, specimen incubation, and imaging of bacterial growth. In this study, we used the WASPLab to validate software that discriminates and segregates positive and negative chromogenic methicillin-resistant Staphylococcus aureus (MRSA) plates by recognition of pigmented colonies. A total of 57,690 swabs submitted for MRSA screening were enrolled in the study. Four sites enrolled specimens following their standard of care. Chromogenic agar used at these sites included MRSASelect (Bio-Rad Laboratories, Redmond, WA), chromID MRSA (bioMérieux, Marcy l'Etoile, France), and CHROMagar MRSA (BD Diagnostics, Sparks, MD). Specimens were plated and incubated using the WASPLab. The digital camera took images at 0 and 16 to 24 h and the WASPLab software determined the presence of positive colonies based on a hue, saturation, and value (HSV) score. If the HSV score fell within a defined threshold, the plate was called positive. The performance of the digital analysis was compared to manual reading. Overall, the digital software had a sensitivity of 100% and a specificity of 90.7% with the specificity ranging between 90.0 and 96.0 across all sites. The results were similar using the three different agars with a sensitivity of 100% and specificity ranging between 90.7 and 92.4%. These data demonstrate that automated digital analysis can be used to accurately sort positive from negative chromogenic agar cultures regardless of the pigmentation produced. Copyright © 2016 Faron et al.

EpHLA: an innovative and user-friendly software automating the HLAMatchmaker algorithm for antibody analysis.

PubMed

Sousa, Luiz Cláudio Demes da Mata; Filho, Herton Luiz Alves Sales; Von Glehn, Cristina de Queiroz Carrascosa; da Silva, Adalberto Socorro; Neto, Pedro de Alcântara dos Santos; de Castro, José Adail Fonseca; do Monte, Semíramis Jamil Hadad

2011-12-01

The global challenge for solid organ transplantation programs is to distribute organs to the highly sensitized recipients. The purpose of this work is to describe and test the functionality of the EpHLA software, a program that automates the analysis of acceptable and unacceptable HLA epitopes on the basis of the HLAMatchmaker algorithm. HLAMatchmaker considers small configurations of polymorphic residues referred to as eplets as essential components of HLA-epitopes. Currently, the analyses require the creation of temporary files and the manual cut and paste of laboratory tests results between electronic spreadsheets, which is time-consuming and prone to administrative errors. The EpHLA software was developed in Object Pascal programming language and uses the HLAMatchmaker algorithm to generate histocompatibility reports. The automated generation of reports requires the integration of files containing the results of laboratory tests (HLA typing, anti-HLA antibody signature) and public data banks (NMDP, IMGT). The integration and the access to this data were accomplished by means of the framework called eDAFramework. The eDAFramework was developed in Object Pascal and PHP and it provides data access functionalities for software developed in these languages. The tool functionality was successfully tested in comparison to actual, manually derived reports of patients from a renal transplantation program with related donors. We successfully developed software, which enables the automated definition of the epitope specificities of HLA antibodies. This new tool will benefit the management of recipient/donor pairs selection for highly sensitized patients. Copyright © 2011 Elsevier B.V. All rights reserved.

ARAM: an automated image analysis software to determine rosetting parameters and parasitaemia in Plasmodium samples.

PubMed

Kudella, Patrick Wolfgang; Moll, Kirsten; Wahlgren, Mats; Wixforth, Achim; Westerhausen, Christoph

2016-04-18

Rosetting is associated with severe malaria and a primary cause of death in Plasmodium falciparum infections. Detailed understanding of this adhesive phenomenon may enable the development of new therapies interfering with rosette formation. For this, it is crucial to determine parameters such as rosetting and parasitaemia of laboratory strains or patient isolates, a bottleneck in malaria research due to the time consuming and error prone manual analysis of specimens. Here, the automated, free, stand-alone analysis software automated rosetting analyzer for micrographs (ARAM) to determine rosetting rate, rosette size distribution as well as parasitaemia with a convenient graphical user interface is presented. Automated rosetting analyzer for micrographs is an executable with two operation modes for automated identification of objects on images. The default mode detects red blood cells and fluorescently labelled parasitized red blood cells by combining an intensity-gradient with a threshold filter. The second mode determines object location and size distribution from a single contrast method. The obtained results are compared with standardized manual analysis. Automated rosetting analyzer for micrographs calculates statistical confidence probabilities for rosetting rate and parasitaemia. Automated rosetting analyzer for micrographs analyses 25 cell objects per second reliably delivering identical results compared to manual analysis. For the first time rosette size distribution is determined in a precise and quantitative manner employing ARAM in combination with established inhibition tests. Additionally ARAM measures the essential observables parasitaemia, rosetting rate and size as well as location of all detected objects and provides confidence intervals for the determined observables. No other existing software solution offers this range of function. The second, non-malaria specific, analysis mode of ARAM offers the functionality to detect arbitrary objects. Automated rosetting analyzer for micrographs has the capability to push malaria research to a more quantitative and statistically significant level with increased reliability due to operator independence. As an installation file for Windows © 7, 8.1 and 10 is available for free, ARAM offers a novel open and easy-to-use platform for the malaria community to elucidate resetting. © 7, 8.1 and 10 is available for free, ARAM offers a novel open and easy-to-use platform for the malaria community to elucidate rosetting.

Improvement of Binary Analysis Components in Automated Malware Analysis Framework

DTIC Science & Technology

2017-02-21

analyze malicious software (malware) with minimum human interaction. The system autonomously analyze malware samples by analyzing malware binary program...AFRL-AFOSR-JP-TR-2017-0018 Improvement of Binary Analysis Components in Automated Malware Analysis Framework Keiji Takeda KEIO UNIVERSITY Final...currently valid OMB control number . PLEASE DO NOT RETURN YOUR FORM TO THE ABOVE ORGANIZATION. 1. REPORT DATE (DD-MM-YYYY)      21-02-2017 2. REPORT

Helios: History and Anatomy of a Successful In-House Enterprise High-Throughput Screening and Profiling Data Analysis System.

PubMed

Gubler, Hanspeter; Clare, Nicholas; Galafassi, Laurent; Geissler, Uwe; Girod, Michel; Herr, Guy

2018-06-01

We describe the main characteristics of the Novartis Helios data analysis software system (Novartis, Basel, Switzerland) for plate-based screening and profiling assays, which was designed and built about 11 years ago. It has been in productive use for more than 10 years and is one of the important standard software applications running for a large user community at all Novartis Institutes for BioMedical Research sites globally. A high degree of automation is reached by embedding the data analysis capabilities into a software ecosystem that deals with the management of samples, plates, and result data files, including automated data loading. The application provides a series of analytical procedures, ranging from very simple to advanced, which can easily be assembled by users in very flexible ways. This also includes the automatic derivation of a large set of quality control (QC) characteristics at every step. Any of the raw, intermediate, and final results and QC-relevant quantities can be easily explored through linked visualizations. Links to global assay metadata management, data warehouses, and an electronic lab notebook system are in place. Automated transfer of relevant data to data warehouses and electronic lab notebook systems are also implemented.

Performing Quantitative Imaging Acquisition, Analysis and Visualization Using the Best of Open Source and Commercial Software Solutions.

PubMed

Shenoy, Shailesh M

2016-07-01

A challenge in any imaging laboratory, especially one that uses modern techniques, is to achieve a sustainable and productive balance between using open source and commercial software to perform quantitative image acquisition, analysis and visualization. In addition to considering the expense of software licensing, one must consider factors such as the quality and usefulness of the software's support, training and documentation. Also, one must consider the reproducibility with which multiple people generate results using the same software to perform the same analysis, how one may distribute their methods to the community using the software and the potential for achieving automation to improve productivity.

Finding the ’RITE’ Acquisition Environment for Navy C2 Software

DTIC Science & Technology

2015-05-01

Boiler plate contract language - Gov purpose Rights • Adding expectation of quality to contracting language • Template SOW’s created Pr...Debugger MCCABE IQ Static Analysis Cyclomatic Complexity and KSLOC. All Languages HP Fortify Security Scan STIG and Vulnerabilities Security & IA...GSSAT (GOTS) Security Scan STIG and Vulnerabilities AutoIT Automated Test Scripting Engine for Automation Functional Testing TestComplete Automated

Design of Inhouse Automated Library Systems.

ERIC Educational Resources Information Center

Cortez, Edwin M.

1984-01-01

Examines six steps inherent to development of in-house automated library system: (1) problem definition, (2) requirement specifications, (3) analysis of alternatives and solutions, (4, 5) design and implementation of hardware and software, and (6) evaluation. Practical method for comparing and weighting options is illustrated and explained. A…

HTAPP: High-Throughput Autonomous Proteomic Pipeline

PubMed Central

Yu, Kebing; Salomon, Arthur R.

2011-01-01

Recent advances in the speed and sensitivity of mass spectrometers and in analytical methods, the exponential acceleration of computer processing speeds, and the availability of genomic databases from an array of species and protein information databases have led to a deluge of proteomic data. The development of a lab-based automated proteomic software platform for the automated collection, processing, storage, and visualization of expansive proteomic datasets is critically important. The high-throughput autonomous proteomic pipeline (HTAPP) described here is designed from the ground up to provide critically important flexibility for diverse proteomic workflows and to streamline the total analysis of a complex proteomic sample. This tool is comprised of software that controls the acquisition of mass spectral data along with automation of post-acquisition tasks such as peptide quantification, clustered MS/MS spectral database searching, statistical validation, and data exploration within a user-configurable lab-based relational database. The software design of HTAPP focuses on accommodating diverse workflows and providing missing software functionality to a wide range of proteomic researchers to accelerate the extraction of biological meaning from immense proteomic data sets. Although individual software modules in our integrated technology platform may have some similarities to existing tools, the true novelty of the approach described here is in the synergistic and flexible combination of these tools to provide an integrated and efficient analysis of proteomic samples. PMID:20336676

A semi-automated volumetric software for segmentation and perfusion parameter quantification of brain tumors using 320-row multidetector computed tomography: a validation study.

PubMed

Chae, Soo Young; Suh, Sangil; Ryoo, Inseon; Park, Arim; Noh, Kyoung Jin; Shim, Hackjoon; Seol, Hae Young

2017-05-01

We developed a semi-automated volumetric software, NPerfusion, to segment brain tumors and quantify perfusion parameters on whole-brain CT perfusion (WBCTP) images. The purpose of this study was to assess the feasibility of the software and to validate its performance compared with manual segmentation. Twenty-nine patients with pathologically proven brain tumors who underwent preoperative WBCTP between August 2012 and February 2015 were included. Three perfusion parameters, arterial flow (AF), equivalent blood volume (EBV), and Patlak flow (PF, which is a measure of permeability of capillaries), of brain tumors were generated by a commercial software and then quantified volumetrically by NPerfusion, which also semi-automatically segmented tumor boundaries. The quantification was validated by comparison with that of manual segmentation in terms of the concordance correlation coefficient and Bland-Altman analysis. With NPerfusion, we successfully performed segmentation and quantified whole volumetric perfusion parameters of all 29 brain tumors that showed consistent perfusion trends with previous studies. The validation of the perfusion parameter quantification exhibited almost perfect agreement with manual segmentation, with Lin concordance correlation coefficients (ρ c ) for AF, EBV, and PF of 0.9988, 0.9994, and 0.9976, respectively. On Bland-Altman analysis, most differences between this software and manual segmentation on the commercial software were within the limit of agreement. NPerfusion successfully performs segmentation of brain tumors and calculates perfusion parameters of brain tumors. We validated this semi-automated segmentation software by comparing it with manual segmentation. NPerfusion can be used to calculate volumetric perfusion parameters of brain tumors from WBCTP.

Application of software technology to automatic test data analysis

NASA Technical Reports Server (NTRS)

Stagner, J. R.

1991-01-01

The verification process for a major software subsystem was partially automated as part of a feasibility demonstration. The methods employed are generally useful and applicable to other types of subsystems. The effort resulted in substantial savings in test engineer analysis time and offers a method for inclusion of automatic verification as a part of regression testing.

An Automation Survival Guide for Media Centers.

ERIC Educational Resources Information Center

Whaley, Roger E.

1989-01-01

Reviews factors that should affect the decision to automate a school media center and offers suggestions for the automation process. Topics discussed include getting the library collection ready for automation, deciding what automated functions are needed, evaluating software vendors, selecting software, and budgeting. (CLB)

Automation for System Safety Analysis

NASA Technical Reports Server (NTRS)

Malin, Jane T.; Fleming, Land; Throop, David; Thronesbery, Carroll; Flores, Joshua; Bennett, Ted; Wennberg, Paul

2009-01-01

This presentation describes work to integrate a set of tools to support early model-based analysis of failures and hazards due to system-software interactions. The tools perform and assist analysts in the following tasks: 1) extract model parts from text for architecture and safety/hazard models; 2) combine the parts with library information to develop the models for visualization and analysis; 3) perform graph analysis and simulation to identify and evaluate possible paths from hazard sources to vulnerable entities and functions, in nominal and anomalous system-software configurations and scenarios; and 4) identify resulting candidate scenarios for software integration testing. There has been significant technical progress in model extraction from Orion program text sources, architecture model derivation (components and connections) and documentation of extraction sources. Models have been derived from Internal Interface Requirements Documents (IIRDs) and FMEA documents. Linguistic text processing is used to extract model parts and relationships, and the Aerospace Ontology also aids automated model development from the extracted information. Visualizations of these models assist analysts in requirements overview and in checking consistency and completeness.

HITCal: a software tool for analysis of video head impulse test responses.

PubMed

Rey-Martinez, Jorge; Batuecas-Caletrio, Angel; Matiño, Eusebi; Perez Fernandez, Nicolás

2015-09-01

The developed software (HITCal) may be a useful tool in the analysis and measurement of the saccadic video head impulse test (vHIT) responses and with the experience obtained during its use the authors suggest that HITCal is an excellent method for enhanced exploration of vHIT outputs. To develop a (software) method to analyze and explore the vHIT responses, mainly saccades. HITCal was written using a computational development program; the function to access a vHIT file was programmed; extended head impulse exploration and measurement tools were created and an automated saccade analysis was developed using an experimental algorithm. For pre-release HITCal laboratory tests, a database of head impulse tests (HITs) was created with the data collected retrospectively in three reference centers. This HITs database was evaluated by humans and was also computed with HITCal. The authors have successfully built HITCal and it has been released as open source software; the developed software was fully operative and all the proposed characteristics were incorporated in the released version. The automated saccades algorithm implemented in HITCal has good concordance with the assessment by human observers (Cohen's kappa coefficient = 0.7).

Software design for automated assembly of truss structures

NASA Technical Reports Server (NTRS)

Herstrom, Catherine L.; Grantham, Carolyn; Allen, Cheryl L.; Doggett, William R.; Will, Ralph W.

1992-01-01

Concern over the limited intravehicular activity time has increased the interest in performing in-space assembly and construction operations with automated robotic systems. A technique being considered at LaRC is a supervised-autonomy approach, which can be monitored by an Earth-based supervisor that intervenes only when the automated system encounters a problem. A test-bed to support evaluation of the hardware and software requirements for supervised-autonomy assembly methods was developed. This report describes the design of the software system necessary to support the assembly process. The software is hierarchical and supports both automated assembly operations and supervisor error-recovery procedures, including the capability to pause and reverse any operation. The software design serves as a model for the development of software for more sophisticated automated systems and as a test-bed for evaluation of new concepts and hardware components.

The Complexity Analysis Tool

DTIC Science & Technology

1988-10-01

overview of the complexity analysis tool ( CAT ), an automated tool which will analyze mission critical computer resources (MCCR) software. CAT is based...84 MAR UNCLASSIFIED SECURITY CLASSIFICATION OF THIS PAGE 19. ABSTRACT: (cont) CAT automates the metric for BASIC (HP-71), ATLAS (EQUATE), Ada (subset...UNIX 5.2). CAT analyzes source code and computes complexity on a module basis. CAT also generates graphic representations of the logic flow paths and

Automated Orbit Determination System (AODS) requirements definition and analysis

NASA Technical Reports Server (NTRS)

Waligora, S. R.; Goorevich, C. E.; Teles, J.; Pajerski, R. S.

1980-01-01

The requirements definition for the prototype version of the automated orbit determination system (AODS) is presented including the AODS requirements at all levels, the functional model as determined through the structured analysis performed during requirements definition, and the results of the requirements analysis. Also specified are the implementation strategy for AODS and the AODS-required external support software system (ADEPT), input and output message formats, and procedures for modifying the requirements.

Automatic structured grid generation using Gridgen (some restrictions apply)

NASA Technical Reports Server (NTRS)

Chawner, John R.; Steinbrenner, John P.

1995-01-01

The authors have noticed in the recent grid generation literature an emphasis on the automation of structured grid generation. The motivation behind such work is clear; grid generation is easily the most despised task in the grid-analyze-visualize triad of computational analysis (CA). However, because grid generation is closely coupled to both the design and analysis software and because quantitative measures of grid quality are lacking, 'push button' grid generation usually results in a compromise between speed, control, and quality. Overt emphasis on automation obscures the substantive issues of providing users with flexible tools for generating and modifying high quality grids in a design environment. In support of this paper's tongue-in-cheek title, many features of the Gridgen software are described. Gridgen is by no stretch of the imagination an automatic grid generator. Despite this fact, the code does utilize many automation techniques that permit interesting regenerative features.

Development of computer-aided design system of elastic sensitive elements of automatic metering devices

NASA Astrophysics Data System (ADS)

Kalinkina, M. E.; Kozlov, A. S.; Labkovskaia, R. I.; Pirozhnikova, O. I.; Tkalich, V. L.; Shmakov, N. A.

2018-05-01

The object of research is the element base of devices of control and automation systems, including in its composition annular elastic sensitive elements, methods of their modeling, calculation algorithms and software complexes for automation of their design processes. The article is devoted to the development of the computer-aided design system of elastic sensitive elements used in weight- and force-measuring automation devices. Based on the mathematical modeling of deformation processes in a solid, as well as the results of static and dynamic analysis, the calculation of elastic elements is given using the capabilities of modern software systems based on numerical simulation. In the course of the simulation, the model was a divided hexagonal grid of finite elements with a maximum size not exceeding 2.5 mm. The results of modal and dynamic analysis are presented in this article.

Progress on automated data analysis algorithms for ultrasonic inspection of composites

NASA Astrophysics Data System (ADS)

Aldrin, John C.; Forsyth, David S.; Welter, John T.

2015-03-01

Progress is presented on the development and demonstration of automated data analysis (ADA) software to address the burden in interpreting ultrasonic inspection data for large composite structures. The automated data analysis algorithm is presented in detail, which follows standard procedures for analyzing signals for time-of-flight indications and backwall amplitude dropout. New algorithms have been implemented to reliably identify indications in time-of-flight images near the front and back walls of composite panels. Adaptive call criteria have also been applied to address sensitivity to variation in backwall signal level, panel thickness variation, and internal signal noise. ADA processing results are presented for a variety of test specimens that include inserted materials and discontinuities produced under poor manufacturing conditions. Software tools have been developed to support both ADA algorithm design and certification, producing a statistical evaluation of indication results and false calls using a matching process with predefined truth tables. Parametric studies were performed to evaluate detection and false call results with respect to varying algorithm settings.

Generic and Automated Data Evaluation in Analytical Measurement.

PubMed

Adam, Martin; Fleischer, Heidi; Thurow, Kerstin

2017-04-01

In the past year, automation has become more and more important in the field of elemental and structural chemical analysis to reduce the high degree of manual operation and processing time as well as human errors. Thus, a high number of data points are generated, which requires fast and automated data evaluation. To handle the preprocessed export data from different analytical devices with software from various vendors offering a standardized solution without any programming knowledge should be preferred. In modern laboratories, multiple users will use this software on multiple personal computers with different operating systems (e.g., Windows, Macintosh, Linux). Also, mobile devices such as smartphones and tablets have gained growing importance. The developed software, Project Analytical Data Evaluation (ADE), is implemented as a web application. To transmit the preevaluated data from the device software to the Project ADE, the exported XML report files are detected and the included data are imported into the entities database using the Data Upload software. Different calculation types of a sample within one measurement series (e.g., method validation) are identified using information tags inside the sample name. The results are presented in tables and diagrams on different information levels (general, detailed for one analyte or sample).

Automated analysis of flow cytometric data for measuring neutrophil CD64 expression using a multi-instrument compatible probability state model.

PubMed

Wong, Linda; Hill, Beth L; Hunsberger, Benjamin C; Bagwell, C Bruce; Curtis, Adam D; Davis, Bruce H

2015-01-01

Leuko64™ (Trillium Diagnostics) is a flow cytometric assay that measures neutrophil CD64 expression and serves as an in vitro indicator of infection/sepsis or the presence of a systemic acute inflammatory response. Leuko64 assay currently utilizes QuantiCALC, a semiautomated software that employs cluster algorithms to define cell populations. The software reduces subjective gating decisions, resulting in interanalyst variability of <5%. We evaluated a completely automated approach to measuring neutrophil CD64 expression using GemStone™ (Verity Software House) and probability state modeling (PSM). Four hundred and fifty-seven human blood samples were processed using the Leuko64 assay. Samples were analyzed on four different flow cytometer models: BD FACSCanto II, BD FACScan, BC Gallios/Navios, and BC FC500. A probability state model was designed to identify calibration beads and three leukocyte subpopulations based on differences in intensity levels of several parameters. PSM automatically calculates CD64 index values for each cell population using equations programmed into the model. GemStone software uses PSM that requires no operator intervention, thus totally automating data analysis and internal quality control flagging. Expert analysis with the predicate method (QuantiCALC) was performed. Interanalyst precision was evaluated for both methods of data analysis. PSM with GemStone correlates well with the expert manual analysis, r(2) = 0.99675 for the neutrophil CD64 index values with no intermethod bias detected. The average interanalyst imprecision for the QuantiCALC method was 1.06% (range 0.00-7.94%), which was reduced to 0.00% with the GemStone PSM. The operator-to-operator agreement in GemStone was a perfect correlation, r(2) = 1.000. Automated quantification of CD64 index values produced results that strongly correlate with expert analysis using a standard gate-based data analysis method. PSM successfully evaluated flow cytometric data generated by multiple instruments across multiple lots of the Leuko64 kit in all 457 cases. The probability-based method provides greater objectivity, higher data analysis speed, and allows for greater precision for in vitro diagnostic flow cytometric assays. © 2015 International Clinical Cytometry Society.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Whitledge, T.E.; Malloy, S.C.; Patton, C.J.

This manual was assembled for use as a guide for analyzing the nutrient content of seawater samples collected in the marine coastal zone of the Northeast United States and the Bering Sea. Some modifications (changes in dilution or sample pump tube sizes) may be necessary to achieve optimum measurements in very pronounced oligotrophic, eutrophic or brackish areas. Information is presented under the following section headings: theory and mechanics of automated analysis; continuous flow system description; operation of autoanalyzer system; cookbook of current nutrient methods; automated analyzer and data analysis software; computer interfacing and hardware modifications; and trouble shooting. The threemore » appendixes are entitled: references and additional reading; manifold components and chemicals; and software listings. (JGB)« less

Manual, semiautomated, and fully automated measurement of the aortic annulus for planning of transcatheter aortic valve replacement (TAVR/TAVI): analysis of interchangeability.

PubMed

Lou, Junyang; Obuchowski, Nancy A; Krishnaswamy, Amar; Popovic, Zoran; Flamm, Scott D; Kapadia, Samir R; Svensson, Lars G; Bolen, Michael A; Desai, Milind Y; Halliburton, Sandra S; Tuzcu, E Murat; Schoenhagen, Paul

2015-01-01

Preprocedural 3-dimensional CT imaging of the aortic annular plane plays a critical role for transcatheter aortic valve replacement (TAVR) planning; however, manual reconstructions are complex. Automated analysis software may improve reproducibility and agreement between readers but is incompletely validated. In 110 TAVR patients (mean age, 81 years; 37% female) undergoing preprocedural multidetector CT, automated reconstruction of the aortic annular plane and planimetry of the annulus was performed with a prototype of now commercially available software (syngo.CT Cardiac Function-Valve Pilot; Siemens Healthcare, Erlangen, Germany). Fully automated, semiautomated, and manual annulus measurements were compared. Intrareader and inter-reader agreement, intermodality agreement, and interchangeability were analyzed. Finally, the impact of these measurements on recommended valve size was evaluated. Semiautomated analysis required major correction in 5 patients (4.5%). In the remaining 95.5%, only minor correction was performed. Mean manual annulus area was significantly smaller than fully automated results (P < .001 for both readers) but similar to semiautomated measurements (5.0 vs 5.4 vs 4.9 cm(2), respectively). The frequency of concordant recommendations for valve size increased if manual analysis was replaced with the semiautomated method (60% agreement was improved to 82.4%; 95% confidence interval for the difference [69.1%-83.4%]). Semiautomated aortic annulus analysis, with minor correction by the user, provides reliable results in the context of TAVR annulus evaluation. Copyright © 2015 Society of Cardiovascular Computed Tomography. Published by Elsevier Inc. All rights reserved.

Technology Infusion of CodeSonar into the Space Network Ground Segment (RII07)

NASA Technical Reports Server (NTRS)

Benson, Markland

2008-01-01

The NASA Software Assurance Research Program (in part) performs studies as to the feasibility of technologies for improving the safety, quality, reliability, cost, and performance of NASA software. This study considers the application of commercial automated source code analysis tools to mission critical ground software that is in the operations and sustainment portion of the product lifecycle.

Report on Automated Semantic Analysis of Scientific and Engineering Codes

NASA Technical Reports Server (NTRS)

Stewart. Maark E. M.; Follen, Greg (Technical Monitor)

2001-01-01

The loss of the Mars Climate Orbiter due to a software error reveals what insiders know: software development is difficult and risky because, in part, current practices do not readily handle the complex details of software. Yet, for scientific software development the MCO mishap represents the tip of the iceberg; few errors are so public, and many errors are avoided with a combination of expertise, care, and testing during development and modification. Further, this effort consumes valuable time and resources even when hardware costs and execution time continually decrease. Software development could use better tools! This lack of tools has motivated the semantic analysis work explained in this report. However, this work has a distinguishing emphasis; the tool focuses on automated recognition of the fundamental mathematical and physical meaning of scientific code. Further, its comprehension is measured by quantitatively evaluating overall recognition with practical codes. This emphasis is necessary if software errors-like the MCO error-are to be quickly and inexpensively avoided in the future. This report evaluates the progress made with this problem. It presents recommendations, describes the approach, the tool's status, the challenges, related research, and a development strategy.

SWIFT MODELLER: a Java based GUI for molecular modeling.

PubMed

Mathur, Abhinav; Shankaracharya; Vidyarthi, Ambarish S

2011-10-01

MODELLER is command line argument based software which requires tedious formatting of inputs and writing of Python scripts which most people are not comfortable with. Also the visualization of output becomes cumbersome due to verbose files. This makes the whole software protocol very complex and requires extensive study of MODELLER manuals and tutorials. Here we describe SWIFT MODELLER, a GUI that automates formatting, scripting and data extraction processes and present it in an interactive way making MODELLER much easier to use than before. The screens in SWIFT MODELLER are designed keeping homology modeling in mind and their flow is a depiction of its steps. It eliminates the formatting of inputs, scripting processes and analysis of verbose output files through automation and makes pasting of the target sequence as the only prerequisite. Jmol (3D structure visualization tool) has been integrated into the GUI which opens and demonstrates the protein data bank files created by the MODELLER software. All files required and created by the software are saved in a folder named after the work instance's date and time of execution. SWIFT MODELLER lowers the skill level required for the software through automation of many of the steps in the original software protocol, thus saving an enormous amount of time per instance and making MODELLER very easy to work with.

Automation of experimental research of waveguide paths induction soldering

NASA Astrophysics Data System (ADS)

Tynchenko, V. S.; Petrenko, V. E.; Kukartsev, V. V.; Tynchenko, V. V.; Antamoshkin, O. A.

2018-05-01

The article presents an automated system of experimental studies of the waveguide paths induction soldering process. The system is a part of additional software for a complex of automated control of the technological process of induction soldering of thin-walled waveguide paths from aluminum alloys, expanding its capabilities. The structure of the software product, the general appearance of the controls and the potential application possibilities are presented. The utility of the developed application by approbation in a series of field experiments was considered and justified. The application of the experimental research system makes it possible to improve the process under consideration, providing the possibility of fine-tuning the control regulators, as well as keeping the statistics of the soldering process in a convenient form for analysis.

Automation Hooks Architecture Trade Study for Flexible Test Orchestration

NASA Technical Reports Server (NTRS)

Lansdowne, Chatwin A.; Maclean, John R.; Graffagnino, Frank J.; McCartney, Patrick A.

2010-01-01

We describe the conclusions of a technology and communities survey supported by concurrent and follow-on proof-of-concept prototyping to evaluate feasibility of defining a durable, versatile, reliable, visible software interface to support strategic modularization of test software development. The objective is that test sets and support software with diverse origins, ages, and abilities can be reliably integrated into test configurations that assemble and tear down and reassemble with scalable complexity in order to conduct both parametric tests and monitored trial runs. The resulting approach is based on integration of three recognized technologies that are currently gaining acceptance within the test industry and when combined provide a simple, open and scalable test orchestration architecture that addresses the objectives of the Automation Hooks task. The technologies are automated discovery using multicast DNS Zero Configuration Networking (zeroconf), commanding and data retrieval using resource-oriented Restful Web Services, and XML data transfer formats based on Automatic Test Markup Language (ATML). This open-source standards-based approach provides direct integration with existing commercial off-the-shelf (COTS) analysis software tools.

Computer-Aided Software Engineering - An approach to real-time software development

NASA Technical Reports Server (NTRS)

Walker, Carrie K.; Turkovich, John J.

1989-01-01

A new software engineering discipline is Computer-Aided Software Engineering (CASE), a technology aimed at automating the software development process. This paper explores the development of CASE technology, particularly in the area of real-time/scientific/engineering software, and a history of CASE is given. The proposed software development environment for the Advanced Launch System (ALS CASE) is described as an example of an advanced software development system for real-time/scientific/engineering (RT/SE) software. The Automated Programming Subsystem of ALS CASE automatically generates executable code and corresponding documentation from a suitably formatted specification of the software requirements. Software requirements are interactively specified in the form of engineering block diagrams. Several demonstrations of the Automated Programming Subsystem are discussed.

Debris Examination Using Ballistic and Radar Integrated Software

NASA Technical Reports Server (NTRS)

Griffith, Anthony; Schottel, Matthew; Lee, David; Scully, Robert; Hamilton, Joseph; Kent, Brian; Thomas, Christopher; Benson, Jonathan; Branch, Eric; Hardman, Paul;

Validation of a new classifier for the automated analysis of the human epidermal growth factor receptor 2 (HER2) gene amplification in breast cancer specimens

PubMed Central

2013-01-01

Amplification of the human epidermal growth factor receptor 2 (HER2) is a prognostic marker for poor clinical outcome and a predictive marker for therapeutic response to targeted therapies in breast cancer patients. With the introduction of anti-HER2 therapies, accurate assessment of HER2 status has become essential. Fluorescence in situ hybridization (FISH) is a widely used technique for the determination of HER2 status in breast cancer. However, the manual signal enumeration is time-consuming. Therefore, several companies like MetaSystem have developed automated image analysis software. Some of these signal enumeration software employ the so called “tile-sampling classifier”, a programming algorithm through which the software quantifies fluorescent signals in images on the basis of square tiles of fixed dimensions. Considering that the size of tile does not always correspond to the size of a single tumor cell nucleus, some users argue that this analysis method might not completely reflect the biology of cells. For that reason, MetaSystems has developed a new classifier which is able to recognize nuclei within tissue sections in order to determine the HER2 amplification status on nuclei basis. We call this new programming algorithm “nuclei-sampling classifier”. In this study, we evaluated the accuracy of the “nuclei-sampling classifier” in determining HER2 gene amplification by FISH in nuclei of breast cancer cells. To this aim, we randomly selected from our cohort 64 breast cancer specimens (32 nonamplified and 32 amplified) and we compared results obtained through manual scoring and through this new classifier. The new classifier automatically recognized individual nuclei. The automated analysis was followed by an optional human correction, during which the user interacted with the software in order to improve the selection of cell nuclei automatically selected. Overall concordance between manual scoring and automated nuclei-sampling analysis was 98.4% (100% for nonamplified cases and 96.9% for amplified cases). However, after human correction, concordance between the two methods was 100%. We conclude that the nuclei-based classifier is a new available tool for automated quantitative HER2 FISH signals analysis in nuclei in breast cancer specimen and it can be used for clinical purposes. PMID:23379971

Tool development in threat assessment: syntax regularization and correlative analysis. Final report Task I and Task II, November 21, 1977-May 21, 1978. [Linguistic analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miron, M.S.; Christopher, C.; Hirshfield, S.

1978-05-01

Psycholinguistics provides crisis managers in nuclear threat incidents with a quantitative methodology which can aid in the determination of threat credibility, authorship identification and perpetrator apprehension. The objective of this contract is to improve and enhance present psycholinguistic software systems by means of newly-developed, computer-automated techniques which significantly extend the technology of automated content and stylistic analysis of nuclear threat. In accordance with this overall objective, the first two contract Tasks have been completed and are reported on in this document. The first Task specifies the development of software support for the purpose of syntax regularization of vocabulary to rootmore » form. The second calls for the exploration and development of alternative approaches to correlative analysis of vocabulary usage.« less

TARDIS: An Automation Framework for JPL Mission Design and Navigation

NASA Technical Reports Server (NTRS)

Roundhill, Ian M.; Kelly, Richard M.

2014-01-01

Mission Design and Navigation at the Jet Propulsion Laboratory has implemented an automation framework tool to assist in orbit determination and maneuver design analysis. This paper describes the lessons learned from previous automation tools and how they have been implemented in this tool. In addition this tool has revealed challenges in software implementation, testing, and user education. This paper describes some of these challenges and invites others to share their experiences.

An Automated Weather Research and Forecasting (WRF)-Based Nowcasting System: Software Description

DTIC Science & Technology

2013-10-01

14. ABSTRACT A Web service /Web interface software package has been engineered to address the need for an automated means to run the Weather Research...An Automated Weather Research and Forecasting (WRF)- Based Nowcasting System: Software Description by Stephen F. Kirby, Brian P. Reen, and...Based Nowcasting System: Software Description Stephen F. Kirby, Brian P. Reen, and Robert E. Dumais Jr. Computational and Information Sciences

An Intelligent Automation Platform for Rapid Bioprocess Design.

PubMed

Wu, Tianyi; Zhou, Yuhong

2014-08-01

Bioprocess development is very labor intensive, requiring many experiments to characterize each unit operation in the process sequence to achieve product safety and process efficiency. Recent advances in microscale biochemical engineering have led to automated experimentation. A process design workflow is implemented sequentially in which (1) a liquid-handling system performs high-throughput wet lab experiments, (2) standalone analysis devices detect the data, and (3) specific software is used for data analysis and experiment design given the user's inputs. We report an intelligent automation platform that integrates these three activities to enhance the efficiency of such a workflow. A multiagent intelligent architecture has been developed incorporating agent communication to perform the tasks automatically. The key contribution of this work is the automation of data analysis and experiment design and also the ability to generate scripts to run the experiments automatically, allowing the elimination of human involvement. A first-generation prototype has been established and demonstrated through lysozyme precipitation process design. All procedures in the case study have been fully automated through an intelligent automation platform. The realization of automated data analysis and experiment design, and automated script programming for experimental procedures has the potential to increase lab productivity. © 2013 Society for Laboratory Automation and Screening.

NASA Tech Briefs, December 1998. Volume 22, No. 12

NASA Technical Reports Server (NTRS)

1998-01-01

Topics include: special coverage section on design and analysis software, and sections on electronic components and circuits, electronic systems, software, materials, mechanics, machinery/automation, manufacturing/fabrication, physical sciences, and special sections of Photonics Tech Briefs, Motion Control Tech briefs and a Hot Technology File 1999 Resource Guide.

CANEapp: a user-friendly application for automated next generation transcriptomic data analysis.

PubMed

Velmeshev, Dmitry; Lally, Patrick; Magistri, Marco; Faghihi, Mohammad Ali

2016-01-13

Next generation sequencing (NGS) technologies are indispensable for molecular biology research, but data analysis represents the bottleneck in their application. Users need to be familiar with computer terminal commands, the Linux environment, and various software tools and scripts. Analysis workflows have to be optimized and experimentally validated to extract biologically meaningful data. Moreover, as larger datasets are being generated, their analysis requires use of high-performance servers. To address these needs, we developed CANEapp (application for Comprehensive automated Analysis of Next-generation sequencing Experiments), a unique suite that combines a Graphical User Interface (GUI) and an automated server-side analysis pipeline that is platform-independent, making it suitable for any server architecture. The GUI runs on a PC or Mac and seamlessly connects to the server to provide full GUI control of RNA-sequencing (RNA-seq) project analysis. The server-side analysis pipeline contains a framework that is implemented on a Linux server through completely automated installation of software components and reference files. Analysis with CANEapp is also fully automated and performs differential gene expression analysis and novel noncoding RNA discovery through alternative workflows (Cuffdiff and R packages edgeR and DESeq2). We compared CANEapp to other similar tools, and it significantly improves on previous developments. We experimentally validated CANEapp's performance by applying it to data derived from different experimental paradigms and confirming the results with quantitative real-time PCR (qRT-PCR). CANEapp adapts to any server architecture by effectively using available resources and thus handles large amounts of data efficiently. CANEapp performance has been experimentally validated on various biological datasets. CANEapp is available free of charge at http://psychiatry.med.miami.edu/research/laboratory-of-translational-rna-genomics/CANE-app . We believe that CANEapp will serve both biologists with no computational experience and bioinformaticians as a simple, timesaving but accurate and powerful tool to analyze large RNA-seq datasets and will provide foundations for future development of integrated and automated high-throughput genomics data analysis tools. Due to its inherently standardized pipeline and combination of automated analysis and platform-independence, CANEapp is an ideal for large-scale collaborative RNA-seq projects between different institutions and research groups.

Demonstration of a software design and statistical analysis methodology with application to patient outcomes data sets

PubMed Central

Mayo, Charles; Conners, Steve; Warren, Christopher; Miller, Robert; Court, Laurence; Popple, Richard

2013-01-01

Purpose: With emergence of clinical outcomes databases as tools utilized routinely within institutions, comes need for software tools to support automated statistical analysis of these large data sets and intrainstitutional exchange from independent federated databases to support data pooling. In this paper, the authors present a design approach and analysis methodology that addresses both issues. Methods: A software application was constructed to automate analysis of patient outcomes data using a wide range of statistical metrics, by combining use of C#.Net and R code. The accuracy and speed of the code was evaluated using benchmark data sets. Results: The approach provides data needed to evaluate combinations of statistical measurements for ability to identify patterns of interest in the data. Through application of the tools to a benchmark data set for dose-response threshold and to SBRT lung data sets, an algorithm was developed that uses receiver operator characteristic curves to identify a threshold value and combines use of contingency tables, Fisher exact tests, Welch t-tests, and Kolmogorov-Smirnov tests to filter the large data set to identify values demonstrating dose-response. Kullback-Leibler divergences were used to provide additional confirmation. Conclusions: The work demonstrates the viability of the design approach and the software tool for analysis of large data sets. PMID:24320426

Demonstration of a software design and statistical analysis methodology with application to patient outcomes data sets.

PubMed

Mayo, Charles; Conners, Steve; Warren, Christopher; Miller, Robert; Court, Laurence; Popple, Richard

2013-11-01

With emergence of clinical outcomes databases as tools utilized routinely within institutions, comes need for software tools to support automated statistical analysis of these large data sets and intrainstitutional exchange from independent federated databases to support data pooling. In this paper, the authors present a design approach and analysis methodology that addresses both issues. A software application was constructed to automate analysis of patient outcomes data using a wide range of statistical metrics, by combining use of C#.Net and R code. The accuracy and speed of the code was evaluated using benchmark data sets. The approach provides data needed to evaluate combinations of statistical measurements for ability to identify patterns of interest in the data. Through application of the tools to a benchmark data set for dose-response threshold and to SBRT lung data sets, an algorithm was developed that uses receiver operator characteristic curves to identify a threshold value and combines use of contingency tables, Fisher exact tests, Welch t-tests, and Kolmogorov-Smirnov tests to filter the large data set to identify values demonstrating dose-response. Kullback-Leibler divergences were used to provide additional confirmation. The work demonstrates the viability of the design approach and the software tool for analysis of large data sets.

Specdata: Automated Analysis Software for Broadband Spectra

NASA Astrophysics Data System (ADS)

Oliveira, Jasmine N.; Martin-Drumel, Marie-Aline; McCarthy, Michael C.

2017-06-01

With the advancement of chirped-pulse techniques, broadband rotational spectra with a few tens to several hundred GHz of spectral coverage are now routinely recorded. When studying multi-component mixtures that might result, for example, with the use of an electrical discharge, lines of new chemical species are often obscured by those of known compounds, and analysis can be laborious. To address this issue, we have developed SPECdata, an open source, interactive tool which is designed to simplify and greatly accelerate the spectral analysis and discovery. Our software tool combines both automated and manual components that free the user from computation, while giving him/her considerable flexibility to assign, manipulate, interpret and export their analysis. The automated - and key - component of the new software is a database query system that rapidly assigns transitions of known species in an experimental spectrum. For each experiment, the software identifies spectral features, and subsequently assigns them to known molecules within an in-house database (Pickett .cat files, list of frequencies...), or those catalogued in Splatalogue (using automatic on-line queries). With suggested assignments, the control is then handed over to the user who can choose to accept, decline or add additional species. Data visualization, statistical information, and interactive widgets assist the user in making decisions about their data. SPECdata has several other useful features intended to improve the user experience. Exporting a full report of the analysis, or a peak file in which assigned lines are removed are among several options. A user may also save their progress to continue at another time. Additional features of SPECdata help the user to maintain and expand their database for future use. A user-friendly interface allows one to search, upload, edit or update catalog or experiment entries.

IMCS reflight certification requirements and design specifications

NASA Technical Reports Server (NTRS)

1984-01-01

The requirements for reflight certification are established. Software requirements encompass the software programs that are resident in the PCC, DEP, PDSS, EC, or any related GSE. A design approach for the reflight software packages is recommended. These designs will be of sufficient detail to permit the implementation of reflight software. The PDSS/IMC Reflight Certification system provides the tools and mechanisms for the user to perform the reflight certification test procedures, test data capture, test data display, and test data analysis. The system as defined will be structured to permit maximum automation of reflight certification procedures and test data analysis.

The Orion GN and C Data-Driven Flight Software Architecture for Automated Sequencing and Fault Recovery

NASA Technical Reports Server (NTRS)

King, Ellis; Hart, Jeremy; Odegard, Ryan

2010-01-01

The Orion Crew Exploration Vehicle (CET) is being designed to include significantly more automation capability than either the Space Shuttle or the International Space Station (ISS). In particular, the vehicle flight software has requirements to accommodate increasingly automated missions throughout all phases of flight. A data-driven flight software architecture will provide an evolvable automation capability to sequence through Guidance, Navigation & Control (GN&C) flight software modes and configurations while maintaining the required flexibility and human control over the automation. This flexibility is a key aspect needed to address the maturation of operational concepts, to permit ground and crew operators to gain trust in the system and mitigate unpredictability in human spaceflight. To allow for mission flexibility and reconfrgurability, a data driven approach is being taken to load the mission event plan as well cis the flight software artifacts associated with the GN&C subsystem. A database of GN&C level sequencing data is presented which manages and tracks the mission specific and algorithm parameters to provide a capability to schedule GN&C events within mission segments. The flight software data schema for performing automated mission sequencing is presented with a concept of operations for interactions with ground and onboard crew members. A prototype architecture for fault identification, isolation and recovery interactions with the automation software is presented and discussed as a forward work item.

Manual versus Automated Rodent Behavioral Assessment: Comparing Efficacy and Ease of Bederson and Garcia Neurological Deficit Scores to an Open Field Video-Tracking System.

PubMed

Desland, Fiona A; Afzal, Aqeela; Warraich, Zuha; Mocco, J

2014-01-01

Animal models of stroke have been crucial in advancing our understanding of the pathophysiology of cerebral ischemia. Currently, the standards for determining neurological deficit in rodents are the Bederson and Garcia scales, manual assessments scoring animals based on parameters ranked on a narrow scale of severity. Automated open field analysis of a live-video tracking system that analyzes animal behavior may provide a more sensitive test. Results obtained from the manual Bederson and Garcia scales did not show significant differences between pre- and post-stroke animals in a small cohort. When using the same cohort, however, post-stroke data obtained from automated open field analysis showed significant differences in several parameters. Furthermore, large cohort analysis also demonstrated increased sensitivity with automated open field analysis versus the Bederson and Garcia scales. These early data indicate use of automated open field analysis software may provide a more sensitive assessment when compared to traditional Bederson and Garcia scales.

Recent development in software and automation tools for high-throughput discovery bioanalysis.

PubMed

Shou, Wilson Z; Zhang, Jun

2012-05-01

Bioanalysis with LC-MS/MS has been established as the method of choice for quantitative determination of drug candidates in biological matrices in drug discovery and development. The LC-MS/MS bioanalytical support for drug discovery, especially for early discovery, often requires high-throughput (HT) analysis of large numbers of samples (hundreds to thousands per day) generated from many structurally diverse compounds (tens to hundreds per day) with a very quick turnaround time, in order to provide important activity and liability data to move discovery projects forward. Another important consideration for discovery bioanalysis is its fit-for-purpose quality requirement depending on the particular experiments being conducted at this stage, and it is usually not as stringent as those required in bioanalysis supporting drug development. These aforementioned attributes of HT discovery bioanalysis made it an ideal candidate for using software and automation tools to eliminate manual steps, remove bottlenecks, improve efficiency and reduce turnaround time while maintaining adequate quality. In this article we will review various recent developments that facilitate automation of individual bioanalytical procedures, such as sample preparation, MS/MS method development, sample analysis and data review, as well as fully integrated software tools that manage the entire bioanalytical workflow in HT discovery bioanalysis. In addition, software tools supporting the emerging high-resolution accurate MS bioanalytical approach are also discussed.

Proteomics Quality Control: Quality Control Software for MaxQuant Results.

PubMed

Bielow, Chris; Mastrobuoni, Guido; Kempa, Stefan

2016-03-04

Mass spectrometry-based proteomics coupled to liquid chromatography has matured into an automatized, high-throughput technology, producing data on the scale of multiple gigabytes per instrument per day. Consequently, an automated quality control (QC) and quality analysis (QA) capable of detecting measurement bias, verifying consistency, and avoiding propagation of error is paramount for instrument operators and scientists in charge of downstream analysis. We have developed an R-based QC pipeline called Proteomics Quality Control (PTXQC) for bottom-up LC-MS data generated by the MaxQuant software pipeline. PTXQC creates a QC report containing a comprehensive and powerful set of QC metrics, augmented with automated scoring functions. The automated scores are collated to create an overview heatmap at the beginning of the report, giving valuable guidance also to nonspecialists. Our software supports a wide range of experimental designs, including stable isotope labeling by amino acids in cell culture (SILAC), tandem mass tags (TMT), and label-free data. Furthermore, we introduce new metrics to score MaxQuant's Match-between-runs (MBR) functionality by which peptide identifications can be transferred across Raw files based on accurate retention time and m/z. Last but not least, PTXQC is easy to install and use and represents the first QC software capable of processing MaxQuant result tables. PTXQC is freely available at https://github.com/cbielow/PTXQC .

Knowledge-based requirements analysis for automating software development

NASA Technical Reports Server (NTRS)

Markosian, Lawrence Z.

1988-01-01

We present a new software development paradigm that automates the derivation of implementations from requirements. In this paradigm, informally-stated requirements are expressed in a domain-specific requirements specification language. This language is machine-understable and requirements expressed in it are captured in a knowledge base. Once the requirements are captured, more detailed specifications and eventually implementations are derived by the system using transformational synthesis. A key characteristic of the process is that the required human intervention is in the form of providing problem- and domain-specific engineering knowledge, not in writing detailed implementations. We describe a prototype system that applies the paradigm in the realm of communication engineering: the prototype automatically generates implementations of buffers following analysis of the requirements on each buffer.

Independent Verification and Validation of Complex User Interfaces: A Human Factors Approach

NASA Technical Reports Server (NTRS)

Whitmore, Mihriban; Berman, Andrea; Chmielewski, Cynthia

1996-01-01

The Usability Testing and Analysis Facility (UTAF) at the NASA Johnson Space Center has identified and evaluated a potential automated software interface inspection tool capable of assessing the degree to which space-related critical and high-risk software system user interfaces meet objective human factors standards across each NASA program and project. Testing consisted of two distinct phases. Phase 1 compared analysis times and similarity of results for the automated tool and for human-computer interface (HCI) experts. In Phase 2, HCI experts critiqued the prototype tool's user interface. Based on this evaluation, it appears that a more fully developed version of the tool will be a promising complement to a human factors-oriented independent verification and validation (IV&V) process.

Workshop on Office Automation and Telecommunication: Applying the Technology.

ERIC Educational Resources Information Center

Mitchell, Bill

This document contains 12 outlines that forecast the office of the future. The outlines cover the following topics: (1) office automation definition and objectives; (2) functional categories of office automation software packages for mini and mainframe computers; (3) office automation-related software for microcomputers; (4) office automation…

Holographic Interferometry and Image Analysis for Aerodynamic Testing

DTIC Science & Technology

1980-09-01

tunnels, (2) development of automated image analysis techniques for reducing quantitative flow-field data from holographic interferograms, and (3...investigation and development of software for the application of digital image analysis to other photographic techniques used in wind tunnel testing.

Operational Based Vision Assessment Automated Vision Test Collection User Guide

DTIC Science & Technology

2017-05-15

repeatability to support correlation analysis. The AVT research grade tests also support interservice, international, industry, and academic partnerships...software, provides information concerning various menu options and operation of the test, and provides a brief description of each of the automated vision...2802, 6 Jun 2017. TABLE OF CONTENTS (concluded) Section Page 7.0 OBVA VISION TEST DESCRIPTIONS

Quantification of Operational Risk Using A Data Mining

NASA Technical Reports Server (NTRS)

Perera, J. Sebastian

1999-01-01

What is Data Mining? - Data Mining is the process of finding actionable information hidden in raw data. - Data Mining helps find hidden patterns, trends, and important relationships often buried in a sea of data - Typically, automated software tools based on advanced statistical analysis and data modeling technology can be utilized to automate the data mining process

Automated data collection in single particle electron microscopy

PubMed Central

Tan, Yong Zi; Cheng, Anchi; Potter, Clinton S.; Carragher, Bridget

2016-01-01

Automated data collection is an integral part of modern workflows in single particle electron microscopy (EM) research. This review surveys the software packages available for automated single particle EM data collection. The degree of automation at each stage of data collection is evaluated, and the capabilities of the software packages are described. Finally, future trends in automation are discussed. PMID:26671944

An Intelligent Automation Platform for Rapid Bioprocess Design

PubMed Central

Wu, Tianyi

2014-01-01

Bioprocess development is very labor intensive, requiring many experiments to characterize each unit operation in the process sequence to achieve product safety and process efficiency. Recent advances in microscale biochemical engineering have led to automated experimentation. A process design workflow is implemented sequentially in which (1) a liquid-handling system performs high-throughput wet lab experiments, (2) standalone analysis devices detect the data, and (3) specific software is used for data analysis and experiment design given the user’s inputs. We report an intelligent automation platform that integrates these three activities to enhance the efficiency of such a workflow. A multiagent intelligent architecture has been developed incorporating agent communication to perform the tasks automatically. The key contribution of this work is the automation of data analysis and experiment design and also the ability to generate scripts to run the experiments automatically, allowing the elimination of human involvement. A first-generation prototype has been established and demonstrated through lysozyme precipitation process design. All procedures in the case study have been fully automated through an intelligent automation platform. The realization of automated data analysis and experiment design, and automated script programming for experimental procedures has the potential to increase lab productivity. PMID:24088579

Information Technology.

ERIC Educational Resources Information Center

Marcum, Deanna; Boss, Richard

1983-01-01

Relates office automation to its application in libraries, discussing computer software packages for microcomputers performing tasks involved in word processing, accounting, statistical analysis, electronic filing cabinets, and electronic mail systems. (EJS)

Extended System Operations Studies for Automated Guideway Transit Systems : Procedure for the Analysis of Representative AGT Deployments

DOT National Transportation Integrated Search

1981-12-01

The purpose of this report is to present a general procedure for using the SOS software to analyze AGT systems. Data to aid the analyst in specifying input information, required as input to the software, are summarized in the appendices. The data are...

Using Rose and Compass for Authentication

DOE Office of Scientific and Technical Information (OSTI.GOV)

White, G

2009-07-09

Many recent non-proliferation software projects include a software authentication component. In this context, 'authentication' is defined as determining that a software package performs only its intended purpose and performs that purpose correctly and reliably over many years. In addition to visual inspection by knowledgeable computer scientists, automated tools are needed to highlight suspicious code constructs both to aid the visual inspection and to guide program development. While many commercial tools are available for portions of the authentication task, they are proprietary, and have limited extensibility. An open-source, extensible tool can be customized to the unique needs of each project. ROSEmore » is an LLNL-developed robust source-to-source analysis and optimization infrastructure currently addressing large, million-line DOE applications in C, C++, and FORTRAN. It continues to be extended to support the automated analysis of binaries (x86, ARM, and PowerPC). We continue to extend ROSE to address a number of security specific requirements and apply it to software authentication for non-proliferation projects. We will give an update on the status of our work.« less

The Design and Development of a Web-Interface for the Software Engineering Automation System

DTIC Science & Technology

2001-09-01

application on the Internet. 14. SUBJECT TERMS Computer Aided Prototyping, Real Time Systems , Java 15. NUMBER OF...difficult. Developing the entire system only to find it does not meet the customer’s needs is a tremendous waste of time. Real - time systems need a...software prototyping is an iterative software development methodology utilized to improve the analysis and design of real - time systems [2]. One

Industrial applications of automated X-ray inspection

NASA Astrophysics Data System (ADS)

Shashishekhar, N.

2015-03-01

Many industries require that 100% of manufactured parts be X-ray inspected. Factors such as high production rates, focus on inspection quality, operator fatigue and inspection cost reduction translate to an increasing need for automating the inspection process. Automated X-ray inspection involves the use of image processing algorithms and computer software for analysis and interpretation of X-ray images. This paper presents industrial applications and illustrative case studies of automated X-ray inspection in areas such as automotive castings, fuel plates, air-bag inflators and tires. It is usually necessary to employ application-specific automated inspection strategies and techniques, since each application has unique characteristics and interpretation requirements.

Performance of Automated Software in the Assessment of Segmental Left Ventricular Function in Cardiac CT: Comparison with Cardiac Magnetic Resonance.

PubMed

Wang, Rui; Meinel, Felix G; Schoepf, U Joseph; Canstein, Christian; Spearman, James V; De Cecco, Carlo N

2015-12-01

To evaluate the accuracy, reliability and time saving potential of a novel cardiac CT (CCT)-based, automated software for the assessment of segmental left ventricular function compared to visual and manual quantitative assessment of CCT and cardiac magnetic resonance (CMR). Forty-seven patients with suspected or known coronary artery disease (CAD) were enrolled in the study. Wall thickening was calculated. Segmental LV wall motion was automatically calculated and shown as a colour-coded polar map. Processing time for each method was recorded. Mean wall thickness in both systolic and diastolic phases on polar map, CCT, and CMR was 9.2 ± 0.1 mm and 14.9 ± 0.2 mm, 8.9 ± 0.1 mm and 14.5 ± 0.1 mm, 8.3 ± 0.1 mm and 13.6 ± 0.1 mm, respectively. Mean wall thickening was 68.4 ± 1.5 %, 64.8 ± 1.4 % and 67.1 ± 1.4 %, respectively. Agreement for the assessment of LV wall motion between CCT, CMR and polar maps was good. Bland-Altman plots and ICC indicated good agreement between CCT, CMR and automated polar maps of the diastolic and systolic segmental wall thickness and thickening. The processing time using polar map was significantly decreased compared with CCT and CMR. Automated evaluation of segmental LV function with polar maps provides similar measurements to manual CCT and CMR evaluation, albeit with substantially reduced analysis time. • Cardiac computed tomography (CCT) can accurately assess segmental left ventricular wall function. • A novel automated software permits accurate and fast evaluation of wall function. • The software may improve the clinical implementation of segmental functional analysis.

Quantitative comparison and evaluation of software packages for assessment of abdominal adipose tissue distribution by magnetic resonance imaging.

PubMed

Bonekamp, S; Ghosh, P; Crawford, S; Solga, S F; Horska, A; Brancati, F L; Diehl, A M; Smith, S; Clark, J M

2008-01-01

To examine five available software packages for the assessment of abdominal adipose tissue with magnetic resonance imaging, compare their features and assess the reliability of measurement results. Feature evaluation and test-retest reliability of softwares (NIHImage, SliceOmatic, Analyze, HippoFat and EasyVision) used in manual, semi-automated or automated segmentation of abdominal adipose tissue. A random sample of 15 obese adults with type 2 diabetes. Axial T1-weighted spin echo images centered at vertebral bodies of L2-L3 were acquired at 1.5 T. Five software packages were evaluated (NIHImage, SliceOmatic, Analyze, HippoFat and EasyVision), comparing manual, semi-automated and automated segmentation approaches. Images were segmented into cross-sectional area (CSA), and the areas of visceral (VAT) and subcutaneous adipose tissue (SAT). Ease of learning and use and the design of the graphical user interface (GUI) were rated. Intra-observer accuracy and agreement between the software packages were calculated using intra-class correlation. Intra-class correlation coefficient was used to obtain test-retest reliability. Three of the five evaluated programs offered a semi-automated technique to segment the images based on histogram values or a user-defined threshold. One software package allowed manual delineation only. One fully automated program demonstrated the drawbacks of uncritical automated processing. The semi-automated approaches reduced variability and measurement error, and improved reproducibility. There was no significant difference in the intra-observer agreement in SAT and CSA. The VAT measurements showed significantly lower test-retest reliability. There were some differences between the software packages in qualitative aspects, such as user friendliness. Four out of five packages provided essentially the same results with respect to the inter- and intra-rater reproducibility. Our results using SliceOmatic, Analyze or NIHImage were comparable and could be used interchangeably. Newly developed fully automated approaches should be compared to one of the examined software packages.

Quantitative comparison and evaluation of software packages for assessment of abdominal adipose tissue distribution by magnetic resonance imaging

PubMed Central

Bonekamp, S; Ghosh, P; Crawford, S; Solga, SF; Horska, A; Brancati, FL; Diehl, AM; Smith, S; Clark, JM

2009-01-01

Objective To examine five available software packages for the assessment of abdominal adipose tissue with magnetic resonance imaging, compare their features and assess the reliability of measurement results. Design Feature evaluation and test–retest reliability of softwares (NIHImage, SliceOmatic, Analyze, HippoFat and EasyVision) used in manual, semi-automated or automated segmentation of abdominal adipose tissue. Subjects A random sample of 15 obese adults with type 2 diabetes. Measurements Axial T1-weighted spin echo images centered at vertebral bodies of L2–L3 were acquired at 1.5 T. Five software packages were evaluated (NIHImage, SliceOmatic, Analyze, HippoFat and EasyVision), comparing manual, semi-automated and automated segmentation approaches. Images were segmented into cross-sectional area (CSA), and the areas of visceral (VAT) and subcutaneous adipose tissue (SAT). Ease of learning and use and the design of the graphical user interface (GUI) were rated. Intra-observer accuracy and agreement between the software packages were calculated using intra-class correlation. Intra-class correlation coefficient was used to obtain test–retest reliability. Results Three of the five evaluated programs offered a semi-automated technique to segment the images based on histogram values or a user-defined threshold. One software package allowed manual delineation only. One fully automated program demonstrated the drawbacks of uncritical automated processing. The semi-automated approaches reduced variability and measurement error, and improved reproducibility. There was no significant difference in the intra-observer agreement in SAT and CSA. The VAT measurements showed significantly lower test–retest reliability. There were some differences between the software packages in qualitative aspects, such as user friendliness. Conclusion Four out of five packages provided essentially the same results with respect to the inter- and intra-rater reproducibility. Our results using SliceOmatic, Analyze or NIHImage were comparable and could be used interchangeably. Newly developed fully automated approaches should be compared to one of the examined software packages. PMID:17700582

Automated Software Analysis of Fetal Movement Recorded during a Pregnant Woman's Sleep at Home.

PubMed

Nishihara, Kyoko; Ohki, Noboru; Kamata, Hideo; Ryo, Eiji; Horiuchi, Shigeko

2015-01-01

Fetal movement is an important biological index of fetal well-being. Since 2008, we have been developing an original capacitive acceleration sensor and device that a pregnant woman can easily use to record fetal movement by herself at home during sleep. In this study, we report a newly developed automated software system for analyzing recorded fetal movement. This study will introduce the system and compare its results to those of a manual analysis of the same fetal movement signals (Experiment I). We will also demonstrate an appropriate way to use the system (Experiment II). In Experiment I, fetal movement data reported previously for six pregnant women at 28-38 gestational weeks were used. We evaluated the agreement of the manual and automated analyses for the same 10-sec epochs using prevalence-adjusted bias-adjusted kappa (PABAK) including quantitative indicators for prevalence and bias. The mean PABAK value was 0.83, which can be considered almost perfect. In Experiment II, twelve pregnant women at 24-36 gestational weeks recorded fetal movement at night once every four weeks. Overall, mean fetal movement counts per hour during maternal sleep significantly decreased along with gestational weeks, though individual differences in fetal development were noted. This newly developed automated analysis system can provide important data throughout late pregnancy.

Automated Software Analysis of Fetal Movement Recorded during a Pregnant Woman’s Sleep at Home

PubMed Central

Nishihara, Kyoko; Ohki, Noboru; Kamata, Hideo; Ryo, Eiji; Horiuchi, Shigeko

2015-01-01

Fetal movement is an important biological index of fetal well-being. Since 2008, we have been developing an original capacitive acceleration sensor and device that a pregnant woman can easily use to record fetal movement by herself at home during sleep. In this study, we report a newly developed automated software system for analyzing recorded fetal movement. This study will introduce the system and compare its results to those of a manual analysis of the same fetal movement signals (Experiment I). We will also demonstrate an appropriate way to use the system (Experiment II). In Experiment I, fetal movement data reported previously for six pregnant women at 28-38 gestational weeks were used. We evaluated the agreement of the manual and automated analyses for the same 10-sec epochs using prevalence-adjusted bias-adjusted kappa (PABAK) including quantitative indicators for prevalence and bias. The mean PABAK value was 0.83, which can be considered almost perfect. In Experiment II, twelve pregnant women at 24-36 gestational weeks recorded fetal movement at night once every four weeks. Overall, mean fetal movement counts per hour during maternal sleep significantly decreased along with gestational weeks, though individual differences in fetal development were noted. This newly developed automated analysis system can provide important data throughout late pregnancy. PMID:26083422

ACES: Space shuttle flight software analysis expert system

NASA Technical Reports Server (NTRS)

Satterwhite, R. Scott

1990-01-01

The Analysis Criteria Evaluation System (ACES) is a knowledge based expert system that automates the final certification of the Space Shuttle onboard flight software. Guidance, navigation and control of the Space Shuttle through all its flight phases are accomplished by a complex onboard flight software system. This software is reconfigured for each flight to allow thousands of mission-specific parameters to be introduced and must therefore be thoroughly certified prior to each flight. This certification is performed in ground simulations by executing the software in the flight computers. Flight trajectories from liftoff to landing, including abort scenarios, are simulated and the results are stored for analysis. The current methodology of performing this analysis is repetitive and requires many man-hours. The ultimate goals of ACES are to capture the knowledge of the current experts and improve the quality and reduce the manpower required to certify the Space Shuttle onboard flight software.

Development of computer software for pavement life cycle cost analysis.

DOT National Transportation Integrated Search

1988-01-01

The life cycle cost analysis program (LCCA) is designed to automate and standardize life cycle costing in Virginia. It allows the user to input information necessary for the analysis, and it then completes the calculations and produces a printed copy...

Toward Intelligent Software Defect Detection

NASA Technical Reports Server (NTRS)

Benson, Markland J.

2011-01-01

Source code level software defect detection has gone from state of the art to a software engineering best practice. Automated code analysis tools streamline many of the aspects of formal code inspections but have the drawback of being difficult to construct and either prone to false positives or severely limited in the set of defects that can be detected. Machine learning technology provides the promise of learning software defects by example, easing construction of detectors and broadening the range of defects that can be found. Pinpointing software defects with the same level of granularity as prominent source code analysis tools distinguishes this research from past efforts, which focused on analyzing software engineering metrics data with granularity limited to that of a particular function rather than a line of code.

THRESH—Software for tracking rainfall thresholds for landslide and debris-flow occurrence, user manual

USGS Publications Warehouse

Baum, Rex L.; Fischer, Sarah J.; Vigil, Jacob C.

2018-02-28

Precipitation thresholds are used in many areas to provide early warning of precipitation-induced landslides and debris flows, and the software distribution THRESH is designed for automated tracking of precipitation, including precipitation forecasts, relative to thresholds for landslide occurrence. This software is also useful for analyzing multiyear precipitation records to compare timing of threshold exceedance with dates and times of historical landslides. This distribution includes the main program THRESH for comparing precipitation to several kinds of thresholds, two utility programs, and a small collection of Python and shell scripts to aid the automated collection and formatting of input data and the graphing and further analysis of output results. The software programs can be deployed on computing platforms that support Fortran 95, Python 2, and certain Unix commands. The software handles rainfall intensity-duration thresholds, cumulative recent-antecedent precipitation thresholds, and peak intensity thresholds as well as various measures of antecedent precipitation. Users should have predefined rainfall thresholds before running THRESH.

MEGA-CC: computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis.

PubMed

Kumar, Sudhir; Stecher, Glen; Peterson, Daniel; Tamura, Koichiro

2012-10-15

There is a growing need in the research community to apply the molecular evolutionary genetics analysis (MEGA) software tool for batch processing a large number of datasets and to integrate it into analysis workflows. Therefore, we now make available the computing core of the MEGA software as a stand-alone executable (MEGA-CC), along with an analysis prototyper (MEGA-Proto). MEGA-CC provides users with access to all the computational analyses available through MEGA's graphical user interface version. This includes methods for multiple sequence alignment, substitution model selection, evolutionary distance estimation, phylogeny inference, substitution rate and pattern estimation, tests of natural selection and ancestral sequence inference. Additionally, we have upgraded the source code for phylogenetic analysis using the maximum likelihood methods for parallel execution on multiple processors and cores. Here, we describe MEGA-CC and outline the steps for using MEGA-CC in tandem with MEGA-Proto for iterative and automated data analysis. http://www.megasoftware.net/.

Optical Coherence Tomography in the UK Biobank Study - Rapid Automated Analysis of Retinal Thickness for Large Population-Based Studies.

PubMed

Keane, Pearse A; Grossi, Carlota M; Foster, Paul J; Yang, Qi; Reisman, Charles A; Chan, Kinpui; Peto, Tunde; Thomas, Dhanes; Patel, Praveen J

2016-01-01

To describe an approach to the use of optical coherence tomography (OCT) imaging in large, population-based studies, including methods for OCT image acquisition, storage, and the remote, rapid, automated analysis of retinal thickness. In UK Biobank, OCT images were acquired between 2009 and 2010 using a commercially available "spectral domain" OCT device (3D OCT-1000, Topcon). Images were obtained using a raster scan protocol, 6 mm x 6 mm in area, and consisting of 128 B-scans. OCT image sets were stored on UK Biobank servers in a central repository, adjacent to high performance computers. Rapid, automated analysis of retinal thickness was performed using custom image segmentation software developed by the Topcon Advanced Biomedical Imaging Laboratory (TABIL). This software employs dual-scale gradient information to allow for automated segmentation of nine intraretinal boundaries in a rapid fashion. 67,321 participants (134,642 eyes) in UK Biobank underwent OCT imaging of both eyes as part of the ocular module. 134,611 images were successfully processed with 31 images failing segmentation analysis due to corrupted OCT files or withdrawal of subject consent for UKBB study participation. Average time taken to call up an image from the database and complete segmentation analysis was approximately 120 seconds per data set per login, and analysis of the entire dataset was completed in approximately 28 days. We report an approach to the rapid, automated measurement of retinal thickness from nearly 140,000 OCT image sets from the UK Biobank. In the near future, these measurements will be publically available for utilization by researchers around the world, and thus for correlation with the wealth of other data collected in UK Biobank. The automated analysis approaches we describe may be of utility for future large population-based epidemiological studies, clinical trials, and screening programs that employ OCT imaging.

Optical Coherence Tomography in the UK Biobank Study – Rapid Automated Analysis of Retinal Thickness for Large Population-Based Studies

PubMed Central

Grossi, Carlota M.; Foster, Paul J.; Yang, Qi; Reisman, Charles A.; Chan, Kinpui; Peto, Tunde; Thomas, Dhanes; Patel, Praveen J.

2016-01-01

Purpose To describe an approach to the use of optical coherence tomography (OCT) imaging in large, population-based studies, including methods for OCT image acquisition, storage, and the remote, rapid, automated analysis of retinal thickness. Methods In UK Biobank, OCT images were acquired between 2009 and 2010 using a commercially available “spectral domain” OCT device (3D OCT-1000, Topcon). Images were obtained using a raster scan protocol, 6 mm x 6 mm in area, and consisting of 128 B-scans. OCT image sets were stored on UK Biobank servers in a central repository, adjacent to high performance computers. Rapid, automated analysis of retinal thickness was performed using custom image segmentation software developed by the Topcon Advanced Biomedical Imaging Laboratory (TABIL). This software employs dual-scale gradient information to allow for automated segmentation of nine intraretinal boundaries in a rapid fashion. Results 67,321 participants (134,642 eyes) in UK Biobank underwent OCT imaging of both eyes as part of the ocular module. 134,611 images were successfully processed with 31 images failing segmentation analysis due to corrupted OCT files or withdrawal of subject consent for UKBB study participation. Average time taken to call up an image from the database and complete segmentation analysis was approximately 120 seconds per data set per login, and analysis of the entire dataset was completed in approximately 28 days. Conclusions We report an approach to the rapid, automated measurement of retinal thickness from nearly 140,000 OCT image sets from the UK Biobank. In the near future, these measurements will be publically available for utilization by researchers around the world, and thus for correlation with the wealth of other data collected in UK Biobank. The automated analysis approaches we describe may be of utility for future large population-based epidemiological studies, clinical trials, and screening programs that employ OCT imaging. PMID:27716837

Reproducibility of a novel echocardiographic 3D automated software for the assessment of mitral valve anatomy.

PubMed

Aquila, Iolanda; González, Ariana; Fernández-Golfín, Covadonga; Rincón, Luis Miguel; Casas, Eduardo; García, Ana; Hinojar, Rocio; Jiménez-Nacher, José Julio; Zamorano, José Luis

2016-05-17

3D transesophageal echocardiography (TEE) is superior to 2D TEE in quantitative anatomic evaluation of the mitral valve (MV) but it shows limitations regarding automatic quantification. Here, we tested the inter-/intra-observer reproducibility of a novel full-automated software in the evaluation of MV anatomy compared to manual 3D assessment. Thirty-six out of 61 screened patients referred to our Cardiac Imaging Unit for TEE were retrospectively included. 3D TEE analysis was performed both manually and with the automated software by two independent operators. Mitral annular area, intercommissural distance, anterior leaflet length and posterior leaflet length were assessed. A significant correlation between both methods was found for all variables: intercommissural diameter (r = 0.84, p < 0.01), mitral annular area (r = 0.94, p > 0, 01), anterior leaflet length (r = 0.83, p < 0.01) and posterior leaflet length (r = 0.67, p < 0.01). Interobserver variability assessed by the intraclass correlation coefficient was superior for the automatic software: intercommisural distance 0.997 vs. 0.76; mitral annular area 0.957 vs. 0.858; anterior leaflet length 0.963 vs. 0.734 and posterior leaflet length 0.936 vs. 0.838. Intraobserver variability was good for both methods with a better level of agreement with the automatic software. The novel 3D automated software is reproducible in MV anatomy assessment. The incorporation of this new tool in clinical MV assessment may improve patient selection and outcomes for MV interventions as well as patient diagnosis and prognosis stratification. Yet, high-quality 3D images are indispensable.

Java Web Start based software for automated quantitative nuclear analysis of prostate cancer and benign prostate hyperplasia.

PubMed

Singh, Swaroop S; Kim, Desok; Mohler, James L

2005-05-11

Androgen acts via androgen receptor (AR) and accurate measurement of the levels of AR protein expression is critical for prostate research. The expression of AR in paired specimens of benign prostate and prostate cancer from 20 African and 20 Caucasian Americans was compared to demonstrate an application of this system. A set of 200 immunopositive and 200 immunonegative nuclei were collected from the images using a macro developed in Image Pro Plus. Linear Discriminant and Logistic Regression analyses were performed on the data to generate classification coefficients. Classification coefficients render the automated image analysis software independent of the type of immunostaining or image acquisition system used. The image analysis software performs local segmentation and uses nuclear shape and size to detect prostatic epithelial nuclei. AR expression is described by (a) percentage of immunopositive nuclei; (b) percentage of immunopositive nuclear area; and (c) intensity of AR expression among immunopositive nuclei or areas. The percent positive nuclei and percent nuclear area were similar by race in both benign prostate hyperplasia and prostate cancer. In prostate cancer epithelial nuclei, African Americans exhibited 38% higher levels of AR immunostaining than Caucasian Americans (two sided Student's t-tests; P < 0.05). Intensity of AR immunostaining was similar between races in benign prostate. The differences measured in the intensity of AR expression in prostate cancer were consistent with previous studies. Classification coefficients are required due to non-standardized immunostaining and image collection methods across medical institutions and research laboratories and helps customize the software for the specimen under study. The availability of a free, automated system creates new opportunities for testing, evaluation and use of this image analysis system by many research groups who study nuclear protein expression.

Novel features and enhancements in BioBin, a tool for the biologically inspired binning and association analysis of rare variants

PubMed Central

Byrska-Bishop, Marta; Wallace, John; Frase, Alexander T; Ritchie, Marylyn D

2018-01-01

Abstract Motivation BioBin is an automated bioinformatics tool for the multi-level biological binning of sequence variants. Herein, we present a significant update to BioBin which expands the software to facilitate a comprehensive rare variant analysis and incorporates novel features and analysis enhancements. Results In BioBin 2.3, we extend our software tool by implementing statistical association testing, updating the binning algorithm, as well as incorporating novel analysis features providing for a robust, highly customizable, and unified rare variant analysis tool. Availability and implementation The BioBin software package is open source and freely available to users at http://www.ritchielab.com/software/biobin-download Contact mdritchie@geisinger.edu Supplementary information Supplementary data are available at Bioinformatics online. PMID:28968757

Elemental misinterpretation in automated analysis of LIBS spectra.

PubMed

Hübert, Waldemar; Ankerhold, Georg

2011-07-01

In this work, the Stark effect is shown to be mainly responsible for wrong elemental allocation by automated laser-induced breakdown spectroscopy (LIBS) software solutions. Due to broadening and shift of an elemental emission line affected by the Stark effect, its measured spectral position might interfere with the line position of several other elements. The micro-plasma is generated by focusing a frequency-doubled 200 mJ pulsed Nd/YAG laser on an aluminum target and furthermore on a brass sample in air at atmospheric pressure. After laser pulse excitation, we have measured the temporal evolution of the Al(II) ion line at 281.6 nm (4s(1)S-3p(1)P) during the decay of the laser-induced plasma. Depending on laser pulse power, the center of the measured line is red-shifted by 130 pm (490 GHz) with respect to the exact line position. In this case, the well-known spectral line positions of two moderate and strong lines of other elements coincide with the actual shifted position of the Al(II) line. Consequently, a time-resolving software analysis can lead to an elemental misinterpretation. To avoid a wrong interpretation of LIBS spectra in automated analysis software for a given LIBS system, we recommend using larger gate delays incorporating Stark broadening parameters and using a range of tolerance, which is non-symmetric around the measured line center. These suggestions may help to improve time-resolving LIBS software promising a smaller probability of wrong elemental identification and making LIBS more attractive for industrial applications.

Automated Simulation For Analysis And Design

NASA Technical Reports Server (NTRS)

Cantwell, E.; Shenk, Tim; Robinson, Peter; Upadhye, R.

1992-01-01

Design Assistant Workstation (DAWN) software being developed to facilitate simulation of qualitative and quantitative aspects of behavior of life-support system in spacecraft, chemical-processing plant, heating and cooling system of large building, or any of variety of systems including interacting process streams and processes. Used to analyze alternative design scenarios or specific designs of such systems. Expert system will automate part of design analysis: reason independently by simulating design scenarios and return to designer with overall evaluations and recommendations.

Using software security analysis to verify the secure socket layer (SSL) protocol

NASA Technical Reports Server (NTRS)

Powell, John D.

2004-01-01

nal Aeronautics and Space Administration (NASA) have tens of thousands of networked computer systems and applications. Software Security vulnerabilities present risks such as lost or corrupted data, information the3, and unavailability of critical systems. These risks represent potentially enormous costs to NASA. The NASA Code Q research initiative 'Reducing Software Security Risk (RSSR) Trough an Integrated Approach '' offers, among its capabilities, formal verification of software security properties, through the use of model based verification (MBV) to address software security risks. [1,2,3,4,5,6] MBV is a formal approach to software assurance that combines analysis of software, via abstract models, with technology, such as model checkers, that provide automation of the mechanical portions of the analysis process. This paper will discuss: The need for formal analysis to assure software systems with respect to software and why testing alone cannot provide it. The means by which MBV with a Flexible Modeling Framework (FMF) accomplishes the necessary analysis task. An example of FMF style MBV in the verification of properties over the Secure Socket Layer (SSL) communication protocol as a demonstration.

Artificial intelligence and expert systems in-flight software testing

NASA Technical Reports Server (NTRS)

Demasie, M. P.; Muratore, J. F.

1991-01-01

The authors discuss the introduction of advanced information systems technologies such as artificial intelligence, expert systems, and advanced human-computer interfaces directly into Space Shuttle software engineering. The reconfiguration automation project (RAP) was initiated to coordinate this move towards 1990s software technology. The idea behind RAP is to automate several phases of the flight software testing procedure and to introduce AI and ES into space shuttle flight software testing. In the first phase of RAP, conventional tools to automate regression testing have already been developed or acquired. There are currently three tools in use.

3D echocardiographic analysis of aortic annulus for transcatheter aortic valve replacement using novel aortic valve quantification software: Comparison with computed tomography.

PubMed

Mediratta, Anuj; Addetia, Karima; Medvedofsky, Diego; Schneider, Robert J; Kruse, Eric; Shah, Atman P; Nathan, Sandeep; Paul, Jonathan D; Blair, John E; Ota, Takeyoshi; Balkhy, Husam H; Patel, Amit R; Mor-Avi, Victor; Lang, Roberto M

2017-05-01

With the increasing use of transcatheter aortic valve replacement (TAVR) in patients with aortic stenosis (AS), computed tomography (CT) remains the standard for annulus sizing. However, 3D transesophageal echocardiography (TEE) has been an alternative in patients with contraindications to CT. We sought to (1) test the feasibility, accuracy, and reproducibility of prototype 3DTEE analysis software (Philips) for aortic annular measurements and (2) compare the new approach to the existing echocardiographic techniques. We prospectively studied 52 patients who underwent gated contrast CT, procedural 3DTEE, and TAVR. 3DTEE images were analyzed using novel semi-automated software designed for 3D measurements of the aortic root, which uses multiplanar reconstruction, similar to CT analysis. Aortic annulus measurements included area, perimeter, and diameter calculations from these measurements. The results were compared to CT-derived values. Additionally, 3D echocardiographic measurements (3D planimetry and mitral valve analysis software adapted for the aortic valve) were also compared to the CT reference values. 3DTEE image quality was sufficient in 90% of patients for aortic annulus measurements using the new software, which were in good agreement with CT (r-values: .89-.91) and small (<4%) inter-modality nonsignificant biases. Repeated measurements showed <10% measurements variability. The new 3D analysis was the more accurate and reproducible of the existing echocardiographic techniques. Novel semi-automated 3DTEE analysis software can accurately measure aortic annulus in patients with severe AS undergoing TAVR, in better agreement with CT than the existing methodology. Accordingly, intra-procedural TEE could potentially replace CT in patients where CT carries significant risk. © 2017, Wiley Periodicals, Inc.

An automation of design and modelling tasks in NX Siemens environment with original software - generator module

NASA Astrophysics Data System (ADS)

Zbiciak, M.; Grabowik, C.; Janik, W.

2015-11-01

Nowadays the design constructional process is almost exclusively aided with CAD/CAE/CAM systems. It is evaluated that nearly 80% of design activities have a routine nature. These design routine tasks are highly susceptible to automation. Design automation is usually made with API tools which allow building original software responsible for adding different engineering activities. In this paper the original software worked out in order to automate engineering tasks at the stage of a product geometrical shape design is presented. The elaborated software works exclusively in NX Siemens CAD/CAM/CAE environment and was prepared in Microsoft Visual Studio with application of the .NET technology and NX SNAP library. The software functionality allows designing and modelling of spur and helicoidal involute gears. Moreover, it is possible to estimate relative manufacturing costs. With the Generator module it is possible to design and model both standard and non-standard gear wheels. The main advantage of the model generated in such a way is its better representation of an involute curve in comparison to those which are drawn in specialized standard CAD systems tools. It comes from fact that usually in CAD systems an involute curve is drawn by 3 points that respond to points located on the addendum circle, the reference diameter of a gear and the base circle respectively. In the Generator module the involute curve is drawn by 11 involute points which are located on and upper the base and the addendum circles therefore 3D gear wheels models are highly accurate. Application of the Generator module makes the modelling process very rapid so that the gear wheel modelling time is reduced to several seconds. During the conducted research the analysis of differences between standard 3 points and 11 points involutes was made. The results and conclusions drawn upon analysis are shown in details.

NASA Tech Briefs, September 1997. Volume 21, No. 9

NASA Technical Reports Server (NTRS)

1997-01-01

Topics include: Data Acquisition and Analysis; Electronic Components and Circuits; Electronic Systems; Physical Sciences; Materials; Computer Software; Mechanics; Machinery/Automation; Manufacturing/Fabrication; Mathematics and Information Sciences.

Automating Security Protocol Analysis

DTIC Science & Technology

2004-03-01

language that allows easy representation of pattern interaction. Using CSP, Lowe tests whether a protocol achieves authentication. In the case of...only to correctly code whatever protocol they intend to evaluate. The tool, OCaml 3.04 [1], translates the protocol into Horn clauses and then...model protocol transactions. One example of automated modeling software is Maude [19]. Maude was the intended language for this research, but Java

Reading Guided by Automated Graphical Representations: How Model-Based Text Visualizations Facilitate Learning in Reading Comprehension Tasks

ERIC Educational Resources Information Center

Pirnay-Dummer, Pablo; Ifenthaler, Dirk

2011-01-01

Our study integrates automated natural language-oriented assessment and analysis methodologies into feasible reading comprehension tasks. With the newly developed T-MITOCAR toolset, prose text can be automatically converted into an association net which has similarities to a concept map. The "text to graph" feature of the software is based on…

Automated Hazard Analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Riddle, F. J.

2003-06-26

The Automated Hazard Analysis (AHA) application is a software tool used to conduct job hazard screening and analysis of tasks to be performed in Savannah River Site facilities. The AHA application provides a systematic approach to the assessment of safety and environmental hazards associated with specific tasks, and the identification of controls regulations, and other requirements needed to perform those tasks safely. AHA is to be integrated into existing Savannah River site work control and job hazard analysis processes. Utilization of AHA will improve the consistency and completeness of hazard screening and analysis, and increase the effectiveness of the workmore » planning process.« less

Automated PCR setup for forensic casework samples using the Normalization Wizard and PCR Setup robotic methods.

PubMed

Greenspoon, S A; Sykes, K L V; Ban, J D; Pollard, A; Baisden, M; Farr, M; Graham, N; Collins, B L; Green, M M; Christenson, C C

2006-12-20

Human genome, pharmaceutical and research laboratories have long enjoyed the application of robotics to performing repetitive laboratory tasks. However, the utilization of robotics in forensic laboratories for processing casework samples is relatively new and poses particular challenges. Since the quantity and quality (a mixture versus a single source sample, the level of degradation, the presence of PCR inhibitors) of the DNA contained within a casework sample is unknown, particular attention must be paid to procedural susceptibility to contamination, as well as DNA yield, especially as it pertains to samples with little biological material. The Virginia Department of Forensic Science (VDFS) has successfully automated forensic casework DNA extraction utilizing the DNA IQ(trade mark) System in conjunction with the Biomek 2000 Automation Workstation. Human DNA quantitation is also performed in a near complete automated fashion utilizing the AluQuant Human DNA Quantitation System and the Biomek 2000 Automation Workstation. Recently, the PCR setup for casework samples has been automated, employing the Biomek 2000 Automation Workstation and Normalization Wizard, Genetic Identity version, which utilizes the quantitation data, imported into the software, to create a customized automated method for DNA dilution, unique to that plate of DNA samples. The PCR Setup software method, used in conjunction with the Normalization Wizard method and written for the Biomek 2000, functions to mix the diluted DNA samples, transfer the PCR master mix, and transfer the diluted DNA samples to PCR amplification tubes. Once the process is complete, the DNA extracts, still on the deck of the robot in PCR amplification strip tubes, are transferred to pre-labeled 1.5 mL tubes for long-term storage using an automated method. The automation of these steps in the process of forensic DNA casework analysis has been accomplished by performing extensive optimization, validation and testing of the software methods.

Experimental research control software system

NASA Astrophysics Data System (ADS)

Cohn, I. A.; Kovalenko, A. G.; Vystavkin, A. N.

2014-05-01

A software system, intended for automation of a small scale research, has been developed. The software allows one to control equipment, acquire and process data by means of simple scripts. The main purpose of that development is to increase experiment automation easiness, thus significantly reducing experimental setup automation efforts. In particular, minimal programming skills are required and supervisors have no reviewing troubles. Interactions between scripts and equipment are managed automatically, thus allowing to run multiple scripts simultaneously. Unlike well-known data acquisition commercial software systems, the control is performed by an imperative scripting language. This approach eases complex control and data acquisition algorithms implementation. A modular interface library performs interaction with external interfaces. While most widely used interfaces are already implemented, a simple framework is developed for fast implementations of new software and hardware interfaces. While the software is in continuous development with new features being implemented, it is already used in our laboratory for automation of a helium-3 cryostat control and data acquisition. The software is open source and distributed under Gnu Public License.

Automated Software Vulnerability Analysis

NASA Astrophysics Data System (ADS)

Sezer, Emre C.; Kil, Chongkyung; Ning, Peng

Despite decades of research, software continues to have vulnerabilities. Successful exploitations of these vulnerabilities by attackers cost millions of dollars to businesses and individuals. Unfortunately, most effective defensive measures, such as patching and intrusion prevention systems, require an intimate knowledge of the vulnerabilities. Many systems for detecting attacks have been proposed. However, the analysis of the exploited vulnerabilities is left to security experts and programmers. Both the human effortinvolved and the slow analysis process are unfavorable for timely defensive measure to be deployed. The problem is exacerbated by zero-day attacks.

Mathematical support for automated geometry analysis of lathe machining of oblique peakless round-nose tools

NASA Astrophysics Data System (ADS)

Filippov, A. V.; Tarasov, S. Yu; Podgornyh, O. A.; Shamarin, N. N.; Filippova, E. O.

2017-01-01

Automatization of engineering processes requires developing relevant mathematical support and a computer software. Analysis of metal cutting kinematics and tool geometry is a necessary key task at the preproduction stage. This paper is focused on developing a procedure for determining the geometry of oblique peakless round-nose tool lathe machining with the use of vector/matrix transformations. Such an approach allows integration into modern mathematical software packages in distinction to the traditional analytic description. Such an advantage is very promising for developing automated control of the preproduction process. A kinematic criterion for the applicable tool geometry has been developed from the results of this study. The effect of tool blade inclination and curvature on the geometry-dependent process parameters was evaluated.

SpcAudace: Spectroscopic processing and analysis package of Audela software

NASA Astrophysics Data System (ADS)

Mauclaire, Benjamin

2017-11-01

SpcAudace processes long slit spectra with automated pipelines and performs astrophysical analysis of the latter data. These powerful pipelines do all the required steps in one pass: standard preprocessing, masking of bad pixels, geometric corrections, registration, optimized spectrum extraction, wavelength calibration and instrumental response computation and correction. Both high and low resolution long slit spectra are managed for stellar and non-stellar targets. Many types of publication-quality figures can be easily produced: pdf and png plots or annotated time series plots. Astrophysical quantities can be derived from individual or large amount of spectra with advanced functions: from line profile characteristics to equivalent width and periodogram. More than 300 documented functions are available and can be used into TCL scripts for automation. SpcAudace is based on Audela open source software.

Automated SEM-EDS GSR Analysis for Turkish Ammunitions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cakir, Ismail; Uner, H. Bulent

2007-04-23

In this work, Automated Scanning Electron Microscopy with Energy Dispersive X-ray Spectrometry (SEM-EDS) was used to characterize 7.65 and 9mm cartridges Turkish ammunition. All samples were analyzed in a SEM Jeol JSM-5600LV equipped BSE detector and a Link ISIS 300 (EDS). A working distance of 20mm, an accelerating voltage of 20 keV and gunshot residue software was used in all analysis. Automated search resulted in a high number of particles analyzed containing gunshot residues (GSR) unique elements (PbBaSb). The obtained data about the definition of characteristic GSR particles was concordant with other studies on this topic.

Spitzer Telemetry Processing System

NASA Technical Reports Server (NTRS)

Stanboli, Alice; Martinez, Elmain M.; McAuley, James M.

2013-01-01

The Spitzer Telemetry Processing System (SirtfTlmProc) was designed to address objectives of JPL's Multi-mission Image Processing Lab (MIPL) in processing spacecraft telemetry and distributing the resulting data to the science community. To minimize costs and maximize operability, the software design focused on automated error recovery, performance, and information management. The system processes telemetry from the Spitzer spacecraft and delivers Level 0 products to the Spitzer Science Center. SirtfTlmProc is a unique system with automated error notification and recovery, with a real-time continuous service that can go quiescent after periods of inactivity. The software can process 2 GB of telemetry and deliver Level 0 science products to the end user in four hours. It provides analysis tools so the operator can manage the system and troubleshoot problems. It automates telemetry processing in order to reduce staffing costs.

A LEAN approach toward automated analysis and data processing of polymers using proton NMR spectroscopy.

PubMed

de Brouwer, Hans; Stegeman, Gerrit

2011-02-01

To maximize utilization of expensive laboratory instruments and to make most effective use of skilled human resources, the entire chain of data processing, calculation, and reporting that is needed to transform raw NMR data into meaningful results was automated. The LEAN process improvement tools were used to identify non-value-added steps in the existing process. These steps were eliminated using an in-house developed software package, which allowed us to meet the key requirement of improving quality and reliability compared with the existing process while freeing up valuable human resources and increasing productivity. Reliability and quality were improved by the consistent data treatment as performed by the software and the uniform administration of results. Automating a single NMR spectrophotometer led to a reduction in operator time of 35%, doubling of the annual sample throughput from 1400 to 2800, and reducing the turn around time from 6 days to less than 2. Copyright © 2011 Society for Laboratory Automation and Screening. Published by Elsevier Inc. All rights reserved.

The Development of Design Tools for Fault Tolerant Quantum Dot Cellular Automata Based Logic

NASA Technical Reports Server (NTRS)

Armstrong, Curtis D.; Humphreys, William M.

2003-01-01

We are developing software to explore the fault tolerance of quantum dot cellular automata gate architectures in the presence of manufacturing variations and device defects. The Topology Optimization Methodology using Applied Statistics (TOMAS) framework extends the capabilities of the A Quantum Interconnected Network Array Simulator (AQUINAS) by adding front-end and back-end software and creating an environment that integrates all of these components. The front-end tools establish all simulation parameters, configure the simulation system, automate the Monte Carlo generation of simulation files, and execute the simulation of these files. The back-end tools perform automated data parsing, statistical analysis and report generation.

VideoHacking: Automated Tracking and Quantification of Locomotor Behavior with Open Source Software and Off-the-Shelf Video Equipment.

PubMed

Conklin, Emily E; Lee, Kathyann L; Schlabach, Sadie A; Woods, Ian G

2015-01-01

Differences in nervous system function can result in differences in behavioral output. Measurements of animal locomotion enable the quantification of these differences. Automated tracking of animal movement is less labor-intensive and bias-prone than direct observation, and allows for simultaneous analysis of multiple animals, high spatial and temporal resolution, and data collection over extended periods of time. Here, we present a new video-tracking system built on Python-based software that is free, open source, and cross-platform, and that can analyze video input from widely available video capture devices such as smartphone cameras and webcams. We validated this software through four tests on a variety of animal species, including larval and adult zebrafish (Danio rerio), Siberian dwarf hamsters (Phodopus sungorus), and wild birds. These tests highlight the capacity of our software for long-term data acquisition, parallel analysis of multiple animals, and application to animal species of different sizes and movement patterns. We applied the software to an analysis of the effects of ethanol on thigmotaxis (wall-hugging) behavior on adult zebrafish, and found that acute ethanol treatment decreased thigmotaxis behaviors without affecting overall amounts of motion. The open source nature of our software enables flexibility, customization, and scalability in behavioral analyses. Moreover, our system presents a free alternative to commercial video-tracking systems and is thus broadly applicable to a wide variety of educational settings and research programs.

IMS - MS Data Extractor

DOE Office of Scientific and Technical Information (OSTI.GOV)

2015-10-20

An automated drift time extraction and computed associated collision cross section software tool for small molecule analysis with ion mobility spectrometry-mass spectrometry (IMS-MS). The software automatically extracts drift times and computes associated collision cross sections for small molecules analyzed using ion mobility spectrometry-mass spectrometry (IMS-MS) based on a target list of expected ions provided by the user.

Automated system for the on-line monitoring of powder blending processes using near-infrared spectroscopy. Part I. System development and control.

PubMed

Hailey, P A; Doherty, P; Tapsell, P; Oliver, T; Aldridge, P K

1996-03-01

An automated system for the on-line monitoring of powder blending processes is described. The system employs near-infrared (NIR) spectroscopy using fibre-optics and a graphical user interface (GUI) developed in the LabVIEW environment. The complete supervisory control and data analysis (SCADA) software controls blender and spectrophotometer operation and performs statistical spectral data analysis in real time. A data analysis routine using standard deviation is described to demonstrate an approach to the real-time determination of blend homogeneity.

CognitionMaster: an object-based image analysis framework

PubMed Central

2013-01-01

Background Automated image analysis methods are becoming more and more important to extract and quantify image features in microscopy-based biomedical studies and several commercial or open-source tools are available. However, most of the approaches rely on pixel-wise operations, a concept that has limitations when high-level object features and relationships between objects are studied and if user-interactivity on the object-level is desired. Results In this paper we present an open-source software that facilitates the analysis of content features and object relationships by using objects as basic processing unit instead of individual pixels. Our approach enables also users without programming knowledge to compose “analysis pipelines“ that exploit the object-level approach. We demonstrate the design and use of example pipelines for the immunohistochemistry-based cell proliferation quantification in breast cancer and two-photon fluorescence microscopy data about bone-osteoclast interaction, which underline the advantages of the object-based concept. Conclusions We introduce an open source software system that offers object-based image analysis. The object-based concept allows for a straight-forward development of object-related interactive or fully automated image analysis solutions. The presented software may therefore serve as a basis for various applications in the field of digital image analysis. PMID:23445542

Accuracy and reproducibility of aortic annular measurements obtained from echocardiographic 3D manual and semi-automated software analyses in patients referred for transcatheter aortic valve implantation: implication for prosthesis size selection.

PubMed

Stella, Stefano; Italia, Leonardo; Geremia, Giulia; Rosa, Isabella; Ancona, Francesco; Marini, Claudia; Capogrosso, Cristina; Giglio, Manuela; Montorfano, Matteo; Latib, Azeem; Margonato, Alberto; Colombo, Antonio; Agricola, Eustachio

2018-02-06

A 3D transoesophageal echocardiography (3D-TOE) reconstruction tool has recently been introduced. The system automatically configures a geometric model of the aortic root and performs quantitative analysis of these structures. We compared the measurements of the aortic annulus (AA) obtained by semi-automated 3D-TOE quantitative software and manual analysis vs. multislice computed tomography (MSCT) ones. One hundred and seventy-five patients (mean age 81.3 ± 6.3 years, 77 men) who underwent both MSCT and 3D-TOE for annulus assessment before transcatheter aortic valve implantation were analysed. Hypothetical prosthetic valve sizing was evaluated using the 3D manual, semi-automated measurements using manufacturer-recommended CT-based sizing algorithm as gold standard. Good correlation between 3D-TOE methods vs. MSCT measurements was found, but the semi-automated analysis demonstrated slightly better correlations for AA major diameter (r = 0.89), perimeter (r = 0.89), and area (r = 0.85) (all P < 0.0001) than manual one. Both 3D methods underestimated the MSCT measurements, but semi-automated measurements showed narrower limits of agreement and lesser bias than manual measurements for most of AA parameters. On average, 3D-TOE semi-automated major diameter, area, and perimeter underestimated the respective MSCT measurements by 7.4%, 3.5%, and 4.4%, respectively, whereas minor diameter was overestimated by 0.3%. Moderate agreement for valve sizing for both 3D-TOE techniques was found: Kappa agreement 0.5 for both semi-automated and manual analysis. Interobserver and intraobserver agreements for the AA measurements were excellent for both techniques (intraclass correlation coefficients for all parameters >0.80). The 3D-TOE semi-automated analysis of AA is feasible and reliable and can be used in clinical practice as an alternative to MSCT for AA assessment. Published on behalf of the European Society of Cardiology. All rights reserved. © The Author(s) 2018. For permissions, please email: journals.permissions@oup.com.

Why people download the freeware AIDA v4.3a diabetes software program: a proof-of-concept semi-automated analysis.

PubMed

Lehmann, Eldon D

2003-01-01

AIDA is a diabetes-computing program freely available at www.2aida.org on the Web. The software is intended to serve as an educational support tool and can be used by anyone who has an interest in diabetes, whether they be patients, relatives, health-care professionals, or students. In previous "Diabetes Information Technology & WebWatch" columns various indicators of usage of the AIDA program have been reviewed, and various comments from users of the software have been documented. The purpose of this column is to overview a proof-of-concept semi-automated analysis about why people are downloading the latest version of the AIDA educational diabetes program. AIDA permits the interactive simulation of plasma insulin and blood glucose profiles for teaching, demonstration, self-learning, and research purposes. It has been made freely available, without charge, on the Internet as a noncommercial contribution to continuing diabetes education. Since its launch in 1996 over 300,000 visits have been logged at the main AIDA Website-www.2aida.org-and over 60,000 copies of the AIDA program have been downloaded free-of-charge. This column documents the results of a semi-automated analysis of comments left by Website visitors while they were downloading the AIDA software, before they had a chance to use the program. The Internet-based survey methodology and semi-automated analysis were both found to be robust and reliable. Over a 5-month period (from October 3, 2001 to February 28, 2002) 400 responses were received. During the corresponding period 1,770 actual visits were made to the Website survey page-giving a response rate to this proof-of-concept study of 22.6%. Responses were received from participants in over 54 countries-with nearly half of these (n = 194; 48.5%) originating from the United States, United Kingdom, and Canada; 208 responses (52.0%) were received from patients with diabetes, 50 (12.5%) from doctors, 49 (12.3%) from relatives of patients, with fewer responses from students, diabetes educators, nurses, pharmacists, and other end users. The semi-automated analysis adopted for this study has re-affirmed the feasibility of using the Internet to obtain free-text comments, at no real cost, from a substantial number of medical software downloaders/users. The survey has also offered some insight into why members of the public continue to turn to the Internet for medical information. Furthermore it has provided useful information about why people are actually downloading the AIDA v4.3a interactive educational "virtual diabetes patient" simulator.

PIV/HPIV Film Analysis Software Package

NASA Technical Reports Server (NTRS)

Blackshire, James L.

1997-01-01

A PIV/HPIV film analysis software system was developed that calculates the 2-dimensional spatial autocorrelations of subregions of Particle Image Velocimetry (PIV) or Holographic Particle Image Velocimetry (HPIV) film recordings. The software controls three hardware subsystems including (1) a Kodak Megaplus 1.4 camera and EPIX 4MEG framegrabber subsystem, (2) an IEEE/Unidex 11 precision motion control subsystem, and (3) an Alacron I860 array processor subsystem. The software runs on an IBM PC/AT host computer running either the Microsoft Windows 3.1 or Windows 95 operating system. It is capable of processing five PIV or HPIV displacement vectors per second, and is completely automated with the exception of user input to a configuration file prior to analysis execution for update of various system parameters.

Managing Automation: A Process, Not a Project.

ERIC Educational Resources Information Center

Hoffmann, Ellen

1988-01-01

Discussion of issues in management of library automation includes: (1) hardware, including systems growth and contracts; (2) software changes, vendor relations, local systems, and microcomputer software; (3) item and authority databases; (4) automation and library staff, organizational structure, and managing change; and (5) environmental issues,…

Development of an automated scanning monochromator for sensitivity calibration of the MUSTANG instrument

NASA Astrophysics Data System (ADS)

Rivers, Thane D.

1992-06-01

An Automated Scanning Monochromator was developed using: an Acton Research Corporation (ARC) Monochromator, Ealing Photomultiplier Tube and a Macintosh PC in conjunction with LabVIEW software. The LabVIEW Virtual Instrument written to operate the ARC Monochromator is a mouse driven user friendly program developed for automated spectral data measurements. Resolution and sensitivity of the Automated Scanning Monochromator System were determined experimentally. The Automated monochromator was then used for spectral measurements of a Platinum Lamp. Additionally, the reflectivity curve for a BaSO4 coated screen has been measured. Reflectivity measurements indicate a large discrepancy with expected results. Further analysis of the reflectivity experiment is required for conclusive results.

Detailed requirements document for the integrated structural analysis system, phase B

NASA Technical Reports Server (NTRS)

Rainey, J. A.

1976-01-01

The requirements are defined for a software system entitled integrated Structural Analysis System (ISAS) Phase B which is being developed to provide the user with a tool by which a complete and detailed analysis of a complex structural system can be performed. This software system will allow for automated interface with numerous structural analysis batch programs and for user interaction in the creation, selection, and validation of data. This system will include modifications to the 4 functions developed for ISAS, and the development of 25 new functions. The new functions are described.

Development of a Prototype Automation Simulation Scenario Generator for Air Traffic Management Software Simulations

NASA Technical Reports Server (NTRS)

Khambatta, Cyrus F.

2007-01-01

A technique for automated development of scenarios for use in the Multi-Center Traffic Management Advisor (McTMA) software simulations is described. The resulting software is designed and implemented to automate the generation of simulation scenarios with the intent of reducing the time it currently takes using an observational approach. The software program is effective in achieving this goal. The scenarios created for use in the McTMA simulations are based on data taken from data files from the McTMA system, and were manually edited before incorporation into the simulations to ensure accuracy. Despite the software s overall favorable performance, several key software issues are identified. Proposed solutions to these issues are discussed. Future enhancements to the scenario generator software may address the limitations identified in this paper.

A model-based approach for automated in vitro cell tracking and chemotaxis analyses.

PubMed

Debeir, Olivier; Camby, Isabelle; Kiss, Robert; Van Ham, Philippe; Decaestecker, Christine

2004-07-01

Chemotaxis may be studied in two main ways: 1) counting cells passing through an insert (e.g., using Boyden chambers), and 2) directly observing cell cultures (e.g., using Dunn chambers), both in response to stationary concentration gradients. This article promotes the use of Dunn chambers and in vitro cell-tracking, achieved by video microscopy coupled with automatic image analysis software, in order to extract quantitative and qualitative measurements characterizing the response of cells to a diffusible chemical agent. Previously, we set up a videomicroscopy system coupled with image analysis software that was able to compute cell trajectories from in vitro cell cultures. In the present study, we are introducing a new software increasing the application field of this system to chemotaxis studies. This software is based on an adapted version of the active contour methodology, enabling each cell to be efficiently tracked for hours and resulting in detailed descriptions of individual cell trajectories. The major advantages of this method come from an improved robustness with respect to variability in cell morphologies between different cell lines and dynamical changes in cell shape during cell migration. Moreover, the software includes a very small number of parameters which do not require overly sensitive tuning. Finally, the running time of the software is very short, allowing improved possibilities in acquisition frequency and, consequently, improved descriptions of complex cell trajectories, i.e. trajectories including cell division and cell crossing. We validated this software on several artificial and real cell culture experiments in Dunn chambers also including comparisons with manual (human-controlled) analyses. We developed new software and data analysis tools for automated cell tracking which enable cell chemotaxis to be efficiently analyzed. Copyright 2004 Wiley-Liss, Inc.

Automated Sequence Generation Process and Software

NASA Technical Reports Server (NTRS)

Gladden, Roy

2007-01-01

"Automated sequence generation" (autogen) signifies both a process and software used to automatically generate sequences of commands to operate various spacecraft. The autogen software comprises the autogen script plus the Activity Plan Generator (APGEN) program. APGEN can be used for planning missions and command sequences.

Automated data mining of a proprietary database system for physician quality improvement.

PubMed

Johnstone, Peter A S; Crenshaw, Tim; Cassels, Diane G; Fox, Timothy H

2008-04-01

Physician practice quality improvement is a subject of intense national debate. This report describes using a software data acquisition program to mine an existing, commonly used proprietary radiation oncology database to assess physician performance. Between 2003 and 2004, a manual analysis was performed of electronic portal image (EPI) review records. Custom software was recently developed to mine the record-and-verify database and the review process of EPI at our institution. In late 2006, a report was developed that allowed for immediate review of physician completeness and speed of EPI review for any prescribed period. The software extracted >46,000 EPIs between 2003 and 2007, providing EPI review status and time to review by each physician. Between 2003 and 2007, the department EPI review improved from 77% to 97% (range, 85.4-100%), with a decrease in the mean time to review from 4.2 days to 2.4 days. The initial intervention in 2003 to 2004 was moderately successful in changing the EPI review patterns; it was not repeated because of the time required to perform it. However, the implementation in 2006 of the automated review tool yielded a profound change in practice. Using the software, the automated chart review required approximately 1.5 h for mining and extracting the data for the 4-year period. This study quantified the EPI review process as it evolved during a 4-year period at our institution and found that automation of data retrieval and review simplified and facilitated physician quality improvement.

Creation of a virtual cutaneous tissue bank

NASA Astrophysics Data System (ADS)

LaFramboise, William A.; Shah, Sujal; Hoy, R. W.; Letbetter, D.; Petrosko, P.; Vennare, R.; Johnson, Peter C.

2000-04-01

Cellular and non-cellular constituents of skin contain fundamental morphometric features and structural patterns that correlate with tissue function. High resolution digital image acquisitions performed using an automated system and proprietary software to assemble adjacent images and create a contiguous, lossless, digital representation of individual microscope slide specimens. Serial extraction, evaluation and statistical analysis of cutaneous feature is performed utilizing an automated analysis system, to derive normal cutaneous parameters comprising essential structural skin components. Automated digital cutaneous analysis allows for fast extraction of microanatomic dat with accuracy approximating manual measurement. The process provides rapid assessment of feature both within individual specimens and across sample populations. The images, component data, and statistical analysis comprise a bioinformatics database to serve as an architectural blueprint for skin tissue engineering and as a diagnostic standard of comparison for pathologic specimens.

GiA Roots: software for the high throughput analysis of plant root system architecture.

PubMed

Galkovskyi, Taras; Mileyko, Yuriy; Bucksch, Alexander; Moore, Brad; Symonova, Olga; Price, Charles A; Topp, Christopher N; Iyer-Pascuzzi, Anjali S; Zurek, Paul R; Fang, Suqin; Harer, John; Benfey, Philip N; Weitz, Joshua S

2012-07-26

Characterizing root system architecture (RSA) is essential to understanding the development and function of vascular plants. Identifying RSA-associated genes also represents an underexplored opportunity for crop improvement. Software tools are needed to accelerate the pace at which quantitative traits of RSA are estimated from images of root networks. We have developed GiA Roots (General Image Analysis of Roots), a semi-automated software tool designed specifically for the high-throughput analysis of root system images. GiA Roots includes user-assisted algorithms to distinguish root from background and a fully automated pipeline that extracts dozens of root system phenotypes. Quantitative information on each phenotype, along with intermediate steps for full reproducibility, is returned to the end-user for downstream analysis. GiA Roots has a GUI front end and a command-line interface for interweaving the software into large-scale workflows. GiA Roots can also be extended to estimate novel phenotypes specified by the end-user. We demonstrate the use of GiA Roots on a set of 2393 images of rice roots representing 12 genotypes from the species Oryza sativa. We validate trait measurements against prior analyses of this image set that demonstrated that RSA traits are likely heritable and associated with genotypic differences. Moreover, we demonstrate that GiA Roots is extensible and an end-user can add functionality so that GiA Roots can estimate novel RSA traits. In summary, we show that the software can function as an efficient tool as part of a workflow to move from large numbers of root images to downstream analysis.

Study of Intelligent Secure Chemical Inventory Management System

NASA Astrophysics Data System (ADS)

Shukran, Mohd Afizi Mohd; Naim Abdullah, Muhammad; Nazri Ismail, Mohd; Maskat, Kamaruzaman; Isa, Mohd Rizal Mohd; Shahfee Ishak, Muhammad; Adib Khairuddin, Muhamad

2017-08-01

Chemical inventory management system has been experiencing a new revolution from traditional inventory system which is manual to an automated inventory management system. In this paper, some review of the classic and modern approaches to chemical inventory management system has been discussed. This paper also describe about both type of inventory management. After a comparative analysis of the traditional method and automated method, it can be said that both methods have some distinctive characteristics. Moreover, the automated inventory management method has higher accuracy of calculation because the calculations are handled by software, eliminating possible errors and saving time. The automated inventory system also allows users and administrators to track the availability, location and consumption of chemicals. The study of this paper can provide forceful review analysis support for the chemical inventory management related research.

Faster Aerodynamic Simulation With Cart3D

NASA Technical Reports Server (NTRS)

2003-01-01

A NASA-developed aerodynamic simulation tool is ensuring the safety of future space operations while providing designers and engineers with an automated, highly accurate computer simulation suite. Cart3D, co-winner of NASA's 2002 Software of the Year award, is the result of over 10 years of research and software development conducted by Michael Aftosmis and Dr. John Melton of Ames Research Center and Professor Marsha Berger of the Courant Institute at New York University. Cart3D offers a revolutionary approach to computational fluid dynamics (CFD), the computer simulation of how fluids and gases flow around an object of a particular design. By fusing technological advancements in diverse fields such as mineralogy, computer graphics, computational geometry, and fluid dynamics, the software provides a new industrial geometry processing and fluid analysis capability with unsurpassed automation and efficiency.

Automated Test Environment for a Real-Time Control System

NASA Technical Reports Server (NTRS)

Hall, Ronald O.

1994-01-01

An automated environment with hardware-in-the-loop has been developed by Rocketdyne Huntsville for test of a real-time control system. The target system of application is the man-rated real-time system which controls the Space Shuttle Main Engines (SSME). The primary use of the environment is software verification and validation, but it is also useful for evaluation and analysis of SSME avionics hardware and mathematical engine models. It provides a test bed for the integration of software and hardware. The principles and skills upon which it operates may be applied to other target systems, such as those requiring hardware-in-the-loop simulation and control system development. Potential applications are in problem domains demanding highly reliable software systems requiring testing to formal requirements and verifying successful transition to/from off-nominal system states.

The Design of Software for Three-Phase Induction Motor Test System

NASA Astrophysics Data System (ADS)

Haixiang, Xu; Fengqi, Wu; Jiai, Xue

2017-11-01

The design and development of control system software is important to three-phase induction motor test equipment, which needs to be completely familiar with the test process and the control procedure of test equipment. In this paper, the software is developed according to the national standard (GB/T1032-2005) about three-phase induction motor test method by VB language. The control system and data analysis software and the implement about motor test system are described individually, which has the advantages of high automation and high accuracy.

An Open Source approach to automated hydrological analysis of ungauged drainage basins in Serbia using R and SAGA

NASA Astrophysics Data System (ADS)

Zlatanovic, Nikola; Milovanovic, Irina; Cotric, Jelena

2014-05-01

Drainage basins are for the most part ungauged or poorly gauged not only in Serbia but in most parts of the world, usually due to insufficient funds, but also the decommission of river gauges in upland catchments to focus on downstream areas which are more populated. Very often, design discharges are needed for these streams or rivers where no streamflow data is available, for various applications. Examples include river training works for flood protection measures or erosion control, design of culverts, water supply facilities, small hydropower plants etc. The estimation of discharges in ungauged basins is most often performed using rainfall-runoff models, whose parameters heavily rely on geomorphometric attributes of the basin (e.g. catchment area, elevation, slopes of channels and hillslopes etc.). The calculation of these, as well as other paramaters, is most often done in GIS (Geographic Information System) software environments. This study deals with the application of freely available and open source software and datasets for automating rainfall-runoff analysis of ungauged basins using methodologies currently in use hydrological practice. The R programming language was used for scripting and automating the hydrological calculations, coupled with SAGA GIS (System for Automated Geoscientivic Analysis) for geocomputing functions and terrain analysis. Datasets used in the analyses include the freely available SRTM (Shuttle Radar Topography Mission) terrain data, CORINE (Coordination of Information on the Environment) Land Cover data, as well as soil maps and rainfall data. The choice of free and open source software and datasets makes the project ideal for academic and research purposes and cross-platform projects. The geomorphometric module was tested on more than 100 catchments throughout Serbia and compared to manually calculated values (using topographic maps). The discharge estimation module was tested on 21 catchments where data were available and compared to results obtained by frequency analysis of annual maximum discharge. The geomorphometric module of the calculation system showed excellent results, saving a great deal of time that would otherwise have been spent on manual processing of geospatial data. This type of automated analysis presented in this study will enable a much quicker hydrologic analysis on multiple watersheds, providing the platform for further research into spatial variability of runoff.

On the Automation of the MarkIII Data Analysis System.

NASA Astrophysics Data System (ADS)

Schwegmann, W.; Schuh, H.

1999-03-01

A faster and semiautomatic data analysis is an important contribution to the acceleration of the VLBI procedure. A concept for the automation of one of the most widely used VLBI software packages the MarkIII Data Analysis System was developed. Then, the program PWXCB, which extracts weather and cable calibration data from the station log-files, was automated supplementing the existing Fortran77 program-code. The new program XLOG and its results will be presented. Most of the tasks in the VLBI data analysis are very complex and their automation requires typical knowledge-based techniques. Thus, a knowledge-based system (KBS) for support and guidance of the analyst is being developed using the AI-workbench BABYLON, which is based on methods of artificial intelligence (AI). The advantages of a KBS for the MarkIII Data Analysis System and the required steps to build a KBS will be demonstrated. Examples about the current status of the project will be given, too.

Automated Engineering Design (AED); An approach to automated documentation

NASA Technical Reports Server (NTRS)

Mcclure, C. W.

1970-01-01

The automated engineering design (AED) is reviewed, consisting of a high level systems programming language, a series of modular precoded subroutines, and a set of powerful software machine tools that effectively automate the production and design of new languages. AED is used primarily for development of problem and user-oriented languages. Software production phases are diagramed, and factors which inhibit effective documentation are evaluated.

NASA Tech Briefs, December 1996. Volume 20, No. 12

NASA Technical Reports Server (NTRS)

1996-01-01

Topics: Design and Analysis Software; Electronic Components and Circuits; Electronic Systems; Physical Sciences; Materials; Computer Programs; Mechanics; Machinery/Automation; Manufacturing/Fabrication; Mathematics and Information Sciences; Life Sciences; Books and Reports

24 CFR 908.104 - Requirements.

Code of Federal Regulations, 2010 CFR

2010-04-01

... contracts with a service bureau to provide the system, the software must be periodically updated to.... Housing agencies that currently use automated software packages to transmit Forms HUD-50058 and HUD-50058... software required to develop and maintain an in-house automated data processing system (ADP) used to...

Automating Software Design Metrics.

DTIC Science & Technology

1984-02-01

INTRODUCTION 1 ", ... 0..1 1.2 HISTORICAL PERSPECTIVE High quality software is of interest to both the software engineering com- munity and its users. As...contributions of many other software engineering efforts, most notably [MCC 77] and [Boe 83b], which have defined and refined a framework for quantifying...AUTOMATION OF DESIGN METRICS Software metrics can be useful within the context of an integrated soft- ware engineering environment. The purpose of this

Collection Analysis: Powerful Ways To Collect, Analyze, and Present Your Data.

ERIC Educational Resources Information Center

Hart, Amy

2003-01-01

Discussion of collection analysis in school libraries focuses on the kinds of data used and how to use library automation software to collect the data. Describes the use of Microsoft Excel and its chart-making capabilities to enhance the presentation of the analysis and suggests ways to use collection analysis output. (LRW)

The information protection level assessment system implementation

NASA Astrophysics Data System (ADS)

Trapeznikov, E. V.

2018-04-01

Currently, the threat of various attacks increases significantly as automated systems become more widespread. On the basis of the conducted analysis the information protection level assessment system establishing objective was identified. The paper presents the information protection level assessment software implementation in the information system by applying the programming language C #. In conclusions the software features are identified and experimental results are represented.

Increasing the Number of Replications in Item Response Theory Simulations: Automation through SAS and Disk Operating System

ERIC Educational Resources Information Center

Gagne, Phill; Furlow, Carolyn; Ross, Terris

2009-01-01

In item response theory (IRT) simulation research, it is often necessary to use one software package for data generation and a second software package to conduct the IRT analysis. Because this can substantially slow down the simulation process, it is sometimes offered as a justification for using very few replications. This article provides…

Leaf-GP: an open and automated software application for measuring growth phenotypes for arabidopsis and wheat.

PubMed

Zhou, Ji; Applegate, Christopher; Alonso, Albor Dobon; Reynolds, Daniel; Orford, Simon; Mackiewicz, Michal; Griffiths, Simon; Penfield, Steven; Pullen, Nick

2017-01-01

Plants demonstrate dynamic growth phenotypes that are determined by genetic and environmental factors. Phenotypic analysis of growth features over time is a key approach to understand how plants interact with environmental change as well as respond to different treatments. Although the importance of measuring dynamic growth traits is widely recognised, available open software tools are limited in terms of batch image processing, multiple traits analyses, software usability and cross-referencing results between experiments, making automated phenotypic analysis problematic. Here, we present Leaf-GP (Growth Phenotypes), an easy-to-use and open software application that can be executed on different computing platforms. To facilitate diverse scientific communities, we provide three software versions, including a graphic user interface (GUI) for personal computer (PC) users, a command-line interface for high-performance computer (HPC) users, and a well-commented interactive Jupyter Notebook (also known as the iPython Notebook) for computational biologists and computer scientists. The software is capable of extracting multiple growth traits automatically from large image datasets. We have utilised it in Arabidopsis thaliana and wheat ( Triticum aestivum ) growth studies at the Norwich Research Park (NRP, UK). By quantifying a number of growth phenotypes over time, we have identified diverse plant growth patterns between different genotypes under several experimental conditions. As Leaf-GP has been evaluated with noisy image series acquired by different imaging devices (e.g. smartphones and digital cameras) and still produced reliable biological outputs, we therefore believe that our automated analysis workflow and customised computer vision based feature extraction software implementation can facilitate a broader plant research community for their growth and development studies. Furthermore, because we implemented Leaf-GP based on open Python-based computer vision, image analysis and machine learning libraries, we believe that our software not only can contribute to biological research, but also demonstrates how to utilise existing open numeric and scientific libraries (e.g. Scikit-image, OpenCV, SciPy and Scikit-learn) to build sound plant phenomics analytic solutions, in a efficient and effective way. Leaf-GP is a sophisticated software application that provides three approaches to quantify growth phenotypes from large image series. We demonstrate its usefulness and high accuracy based on two biological applications: (1) the quantification of growth traits for Arabidopsis genotypes under two temperature conditions; and (2) measuring wheat growth in the glasshouse over time. The software is easy-to-use and cross-platform, which can be executed on Mac OS, Windows and HPC, with open Python-based scientific libraries preinstalled. Our work presents the advancement of how to integrate computer vision, image analysis, machine learning and software engineering in plant phenomics software implementation. To serve the plant research community, our modulated source code, detailed comments, executables (.exe for Windows; .app for Mac), and experimental results are freely available at https://github.com/Crop-Phenomics-Group/Leaf-GP/releases.

Technical note on the validation of a semi-automated image analysis software application for estrogen and progesterone receptor detection in breast cancer.

PubMed

Krecsák, László; Micsik, Tamás; Kiszler, Gábor; Krenács, Tibor; Szabó, Dániel; Jónás, Viktor; Császár, Gergely; Czuni, László; Gurzó, Péter; Ficsor, Levente; Molnár, Béla

2011-01-18

The immunohistochemical detection of estrogen (ER) and progesterone (PR) receptors in breast cancer is routinely used for prognostic and predictive testing. Whole slide digitalization supported by dedicated software tools allows quantization of the image objects (e.g. cell membrane, nuclei) and an unbiased analysis of immunostaining results. Validation studies of image analysis applications for the detection of ER and PR in breast cancer specimens provided strong concordance between the pathologist's manual assessment of slides and scoring performed using different software applications. The effectiveness of two connected semi-automated image analysis software (NuclearQuant v. 1.13 application for Pannoramic™ Viewer v. 1.14) for determination of ER and PR status in formalin-fixed paraffin embedded breast cancer specimens immunostained with the automated Leica Bond Max system was studied. First the detection algorithm was calibrated to the scores provided an independent assessors (pathologist), using selected areas from 38 small digital slides (created from 16 cases) containing a mean number of 195 cells. Each cell was manually marked and scored according to the Allred-system combining frequency and intensity scores. The performance of the calibrated algorithm was tested on 16 cases (14 invasive ductal carcinoma, 2 invasive lobular carcinoma) against the pathologist's manual scoring of digital slides. The detection was calibrated to 87 percent object detection agreement and almost perfect Total Score agreement (Cohen's kappa 0.859, quadratic weighted kappa 0.986) from slight or moderate agreement at the start of the study, using the un-calibrated algorithm. The performance of the application was tested against the pathologist's manual scoring of digital slides on 53 regions of interest of 16 ER and PR slides covering all positivity ranges, and the quadratic weighted kappa provided almost perfect agreement (κ = 0.981) among the two scoring schemes. NuclearQuant v. 1.13 application for Pannoramic™ Viewer v. 1.14 software application proved to be a reliable image analysis tool for pathologists testing ER and PR status in breast cancer.

Localization-based super-resolution imaging meets high-content screening.

PubMed

Beghin, Anne; Kechkar, Adel; Butler, Corey; Levet, Florian; Cabillic, Marine; Rossier, Olivier; Giannone, Gregory; Galland, Rémi; Choquet, Daniel; Sibarita, Jean-Baptiste

2017-12-01

Single-molecule localization microscopy techniques have proven to be essential tools for quantitatively monitoring biological processes at unprecedented spatial resolution. However, these techniques are very low throughput and are not yet compatible with fully automated, multiparametric cellular assays. This shortcoming is primarily due to the huge amount of data generated during imaging and the lack of software for automation and dedicated data mining. We describe an automated quantitative single-molecule-based super-resolution methodology that operates in standard multiwell plates and uses analysis based on high-content screening and data-mining software. The workflow is compatible with fixed- and live-cell imaging and allows extraction of quantitative data like fluorophore photophysics, protein clustering or dynamic behavior of biomolecules. We demonstrate that the method is compatible with high-content screening using 3D dSTORM and DNA-PAINT based super-resolution microscopy as well as single-particle tracking.

Using satellite communications for a mobile computer network

NASA Technical Reports Server (NTRS)

Wyman, Douglas J.

1993-01-01

The topics discussed include the following: patrol car automation, mobile computer network, network requirements, network design overview, MCN mobile network software, MCN hub operation, mobile satellite software, hub satellite software, the benefits of patrol car automation, the benefits of satellite mobile computing, and national law enforcement satellite.

Evaluation of software tools for automated identification of neuroanatomical structures in quantitative β-amyloid PET imaging to diagnose Alzheimer's disease.

PubMed

Tuszynski, Tobias; Rullmann, Michael; Luthardt, Julia; Butzke, Daniel; Tiepolt, Solveig; Gertz, Hermann-Josef; Hesse, Swen; Seese, Anita; Lobsien, Donald; Sabri, Osama; Barthel, Henryk

2016-06-01

For regional quantification of nuclear brain imaging data, defining volumes of interest (VOIs) by hand is still the gold standard. As this procedure is time-consuming and operator-dependent, a variety of software tools for automated identification of neuroanatomical structures were developed. As the quality and performance of those tools are poorly investigated so far in analyzing amyloid PET data, we compared in this project four algorithms for automated VOI definition (HERMES Brass, two PMOD approaches, and FreeSurfer) against the conventional method. We systematically analyzed florbetaben brain PET and MRI data of ten patients with probable Alzheimer's dementia (AD) and ten age-matched healthy controls (HCs) collected in a previous clinical study. VOIs were manually defined on the data as well as through the four automated workflows. Standardized uptake value ratios (SUVRs) with the cerebellar cortex as a reference region were obtained for each VOI. SUVR comparisons between ADs and HCs were carried out using Mann-Whitney-U tests, and effect sizes (Cohen's d) were calculated. SUVRs of automatically generated VOIs were correlated with SUVRs of conventionally derived VOIs (Pearson's tests). The composite neocortex SUVRs obtained by manually defined VOIs were significantly higher for ADs vs. HCs (p=0.010, d=1.53). This was also the case for the four tested automated approaches which achieved effect sizes of d=1.38 to d=1.62. SUVRs of automatically generated VOIs correlated significantly with those of the hand-drawn VOIs in a number of brain regions, with regional differences in the degree of these correlations. Best overall correlation was observed in the lateral temporal VOI for all tested software tools (r=0.82 to r=0.95, p<0.001). Automated VOI definition by the software tools tested has a great potential to substitute for the current standard procedure to manually define VOIs in β-amyloid PET data analysis.

An Automated Solar Synoptic Analysis Software System

NASA Astrophysics Data System (ADS)

Hong, S.; Lee, S.; Oh, S.; Kim, J.; Lee, J.; Kim, Y.; Lee, J.; Moon, Y.; Lee, D.

2012-12-01

We have developed an automated software system of identifying solar active regions, filament channels, and coronal holes, those are three major solar sources causing the space weather. Space weather forecasters of NOAA Space Weather Prediction Center produce the solar synoptic drawings as a daily basis to predict solar activities, i.e., solar flares, filament eruptions, high speed solar wind streams, and co-rotating interaction regions as well as their possible effects to the Earth. As an attempt to emulate this process with a fully automated and consistent way, we developed a software system named ASSA(Automated Solar Synoptic Analysis). When identifying solar active regions, ASSA uses high-resolution SDO HMI intensitygram and magnetogram as inputs and providing McIntosh classification and Mt. Wilson magnetic classification of each active region by applying appropriate image processing techniques such as thresholding, morphology extraction, and region growing. At the same time, it also extracts morphological and physical properties of active regions in a quantitative way for the short-term prediction of flares and CMEs. When identifying filament channels and coronal holes, images of global H-alpha network and SDO AIA 193 are used for morphological identification and also SDO HMI magnetograms for quantitative verification. The output results of ASSA are routinely checked and validated against NOAA's daily SRS(Solar Region Summary) and UCOHO(URSIgram code for coronal hole information). A couple of preliminary scientific results are to be presented using available output results. ASSA will be deployed at the Korean Space Weather Center and serve its customers in an operational status by the end of 2012.

Automated Liquid Microjunction Surface Sampling-HPLC-MS/MS Analysis of Drugs and Metabolites in Whole-Body Thin Tissue Sections

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kertesz, Vilmos; Van Berkel, Gary J

A fully automated liquid extraction-based surface sampling system utilizing a commercially available autosampler coupled to high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) detection is reported. Discrete spots selected for droplet-based sampling and automated sample queue generation for both the autosampler and MS were enabled by using in-house developed software. In addition, co-registration of spatially resolved sampling position and HPLC-MS information to generate heatmaps of compounds monitored for subsequent data analysis was also available in the software. The system was evaluated with whole-body thin tissue sections from propranolol dosed rat. The hands-free operation of the system was demonstrated by creating heatmapsmore » of the parent drug and its hydroxypropranolol glucuronide metabolites with 1 mm resolution in the areas of interest. The sample throughput was approximately 5 min/sample defined by the time needed for chromatographic separation. The spatial distributions of both the drug and its metabolites were consistent with previous studies employing other liquid extraction-based surface sampling methodologies.« less

NASA Tech Briefs, December 2004

NASA Technical Reports Server (NTRS)

2004-01-01

opics include: High-Rate Digital Receiver Board; Signal Design for Improved Ranging Among Multiple Transceivers; Automated Analysis, Classification, and Display of Waveforms; Fast-Acquisition/Weak-Signal-Tracking GPS Receiver for HEO; Format for Interchange and Display of 3D Terrain Data; Program Analyzes Radar Altimeter Data; Indoor Navigation using Direction Sensor and Beacons; Software Assists in Responding to Anomalous Conditions; Software for Autonomous Spacecraft Maneuvers; WinPlot; Software for Automated Testing of Mission-Control Displays; Nanocarpets for Trapping Microscopic Particles; Precious-Metal Salt Coatings for Detecting Hydrazines; Amplifying Electrochemical Indicators; Better End-Cap Processing for Oxidation-Resistant Polyimides; Carbon-Fiber Brush Heat Exchangers; Solar-Powered Airplane with Cameras and WLAN; A Resonator for Low-Threshold Frequency Conversion; Masked Proportional Routing; Algorithm Determines Wind Speed and Direction from Venturi-Sensor Data; Feature-Identification and Data-Compression Software; Alternative Attitude Commanding and Control for Precise Spacecraft Landing; Inspecting Friction Stir Welding using Electromagnetic Probes; and Helicity in Supercritical O2/H2 and C7H16/N2 Mixing Layers.

Verification and Validation in a Rapid Software Development Process

NASA Technical Reports Server (NTRS)

Callahan, John R.; Easterbrook, Steve M.

1997-01-01

The high cost of software production is driving development organizations to adopt more automated design and analysis methods such as rapid prototyping, computer-aided software engineering (CASE) tools, and high-level code generators. Even developers of safety-critical software system have adopted many of these new methods while striving to achieve high levels Of quality and reliability. While these new methods may enhance productivity and quality in many cases, we examine some of the risks involved in the use of new methods in safety-critical contexts. We examine a case study involving the use of a CASE tool that automatically generates code from high-level system designs. We show that while high-level testing on the system structure is highly desirable, significant risks exist in the automatically generated code and in re-validating releases of the generated code after subsequent design changes. We identify these risks and suggest process improvements that retain the advantages of rapid, automated development methods within the quality and reliability contexts of safety-critical projects.

SAGA: A project to automate the management of software production systems

NASA Technical Reports Server (NTRS)

Campbell, Roy H.; Beckman-Davies, C. S.; Benzinger, L.; Beshers, G.; Laliberte, D.; Render, H.; Sum, R.; Smith, W.; Terwilliger, R.

1986-01-01

Research into software development is required to reduce its production cost and to improve its quality. Modern software systems, such as the embedded software required for NASA's space station initiative, stretch current software engineering techniques. The requirements to build large, reliable, and maintainable software systems increases with time. Much theoretical and practical research is in progress to improve software engineering techniques. One such technique is to build a software system or environment which directly supports the software engineering process, i.e., the SAGA project, comprising the research necessary to design and build a software development which automates the software engineering process. Progress under SAGA is described.

Development and prospective evaluation of an automated software system for quality control of quantitative 99mTc-MAG3 renal studies.

PubMed

Folks, Russell D; Garcia, Ernest V; Taylor, Andrew T

2007-03-01

Quantitative nuclear renography has numerous potential sources of error. We previously reported the initial development of a computer software module for comprehensively addressing the issue of quality control (QC) in the analysis of radionuclide renal images. The objective of this study was to prospectively test the QC software. The QC software works in conjunction with standard quantitative renal image analysis using a renal quantification program. The software saves a text file that summarizes QC findings as possible errors in user-entered values, calculated values that may be unreliable because of the patient's clinical condition, and problems relating to acquisition or processing. To test the QC software, a technologist not involved in software development processed 83 consecutive nontransplant clinical studies. The QC findings of the software were then tabulated. QC events were defined as technical (study descriptors that were out of range or were entered and then changed, unusually sized or positioned regions of interest, or missing frames in the dynamic image set) or clinical (calculated functional values judged to be erroneous or unreliable). Technical QC events were identified in 36 (43%) of 83 studies. Clinical QC events were identified in 37 (45%) of 83 studies. Specific QC events included starting the camera after the bolus had reached the kidney, dose infiltration, oversubtraction of background activity, and missing frames in the dynamic image set. QC software has been developed to automatically verify user input, monitor calculation of renal functional parameters, summarize QC findings, and flag potentially unreliable values for the nuclear medicine physician. Incorporation of automated QC features into commercial or local renal software can reduce errors and improve technologist performance and should improve the efficiency and accuracy of image interpretation.

Automated flow quantification in valvular heart disease based on backscattered Doppler power analysis: implementation on matrix-array ultrasound imaging systems.

PubMed

Buck, Thomas; Hwang, Shawn M; Plicht, Björn; Mucci, Ronald A; Hunold, Peter; Erbel, Raimund; Levine, Robert A

2008-06-01

Cardiac ultrasound imaging systems are limited in the noninvasive quantification of valvular regurgitation due to indirect measurements and inaccurate hemodynamic assumptions. We recently demonstrated that the principle of integration of backscattered acoustic Doppler power times velocity can be used for flow quantification in valvular regurgitation directly at the vena contracta of a regurgitant flow jet. We now aimed to accomplish implementation of automated Doppler power flow analysis software on a standard cardiac ultrasound system utilizing novel matrix-array transducer technology with detailed description of system requirements, components and software contributing to the system. This system based on a 3.5 MHz, matrix-array cardiac ultrasound scanner (Sonos 5500, Philips Medical Systems) was validated by means of comprehensive experimental signal generator trials, in vitro flow phantom trials and in vivo testing in 48 patients with mitral regurgitation of different severity and etiology using magnetic resonance imaging (MRI) for reference. All measurements displayed good correlation to the reference values, indicating successful implementation of automated Doppler power flow analysis on a matrix-array ultrasound imaging system. Systematic underestimation of effective regurgitant orifice areas >0.65 cm(2) and volumes >40 ml was found due to currently limited Doppler beam width that could be readily overcome by the use of new generation 2D matrix-array technology. Automated flow quantification in valvular heart disease based on backscattered Doppler power can be fully implemented on board a routinely used matrix-array ultrasound imaging systems. Such automated Doppler power flow analysis of valvular regurgitant flow directly, noninvasively, and user independent overcomes the practical limitations of current techniques.

SAGA: A project to automate the management of software production systems

NASA Technical Reports Server (NTRS)

Campbell, R. H.; Badger, W.; Beckman, C. S.; Beshers, G.; Hammerslag, D.; Kimball, J.; Kirslis, P. A.; Render, H.; Richards, P.; Terwilliger, R.

1984-01-01

The project to automate the management of software production systems is described. The SAGA system is a software environment that is designed to support most of the software development activities that occur in a software lifecycle. The system can be configured to support specific software development applications using given programming languages, tools, and methodologies. Meta-tools are provided to ease configuration. Several major components of the SAGA system are completed to prototype form. The construction methods are described.

Automated CT Scan Scores of Bronchiectasis and Air Trapping in Cystic Fibrosis

PubMed Central

Swiercz, Waldemar; Heltshe, Sonya L.; Anthony, Margaret M.; Szefler, Paul; Klein, Rebecca; Strain, John; Brody, Alan S.; Sagel, Scott D.

2014-01-01

Background: Computer analysis of high-resolution CT (HRCT) scans may improve the assessment of structural lung injury in children with cystic fibrosis (CF). The goal of this cross-sectional pilot study was to validate automated, observer-independent image analysis software to establish objective, simple criteria for bronchiectasis and air trapping. Methods: HRCT scans of the chest were performed in 35 children with CF and compared with scans from 12 disease control subjects. Automated image analysis software was developed to count visible airways on inspiratory images and to measure a low attenuation density (LAD) index on expiratory images. Among the children with CF, relationships among automated measures, Brody HRCT scanning scores, lung function, and sputum markers of inflammation were assessed. Results: The number of total, central, and peripheral airways on inspiratory images and LAD (%) on expiratory images were significantly higher in children with CF compared with control subjects. Among subjects with CF, peripheral airway counts correlated strongly with Brody bronchiectasis scores by two raters (r = 0.86, P < .0001; r = 0.91, P < .0001), correlated negatively with lung function, and were positively associated with sputum free neutrophil elastase activity. LAD (%) correlated with Brody air trapping scores (r = 0.83, P < .0001; r = 0.69, P < .0001) but did not correlate with lung function or sputum inflammatory markers. Conclusions: Quantitative airway counts and LAD (%) on HRCT scans appear to be useful surrogates for bronchiectasis and air trapping in children with CF. Our automated methodology provides objective quantitative measures of bronchiectasis and air trapping that may serve as end points in CF clinical trials. PMID:24114359

Data fusion for automated non-destructive inspection

PubMed Central

Brierley, N.; Tippetts, T.; Cawley, P.

2014-01-01

In industrial non-destructive evaluation (NDE), it is increasingly common for data acquisition to be automated, driving a recent substantial increase in the availability of data. The collected data need to be analysed, typically necessitating the painstaking manual labour of a skilled operator. Moreover, in automated NDE a region of an inspected component is typically interrogated several times, be it within a single data channel due to multiple probe passes, across several channels acquired simultaneously or over the course of repeated inspections. The systematic combination of these diverse readings is recognized to offer an opportunity to improve the reliability of the inspection, but is not achievable in a manual analysis. This paper describes a data-fusion-based software framework providing a partial automation capability, allowing component regions to be declared defect-free to a very high probability while readily identifying defect indications, thereby optimizing the use of the operator's time. The system is designed to applicable to a wide range of automated NDE scenarios, but the processing is exemplified using the industrial ultrasonic immersion inspection of aerospace turbine discs. Results obtained for industrial datasets demonstrate an orders-of-magnitude reduction in false-call rates, for a given probability of detection, achievable using the developed software system. PMID:25002828

Simulation based optimization on automated fibre placement process

NASA Astrophysics Data System (ADS)

Lei, Shi

2018-02-01

In this paper, a software simulation (Autodesk TruPlan & TruFiber) based method is proposed to optimize the automate fibre placement (AFP) process. Different types of manufacturability analysis are introduced to predict potential defects. Advanced fibre path generation algorithms are compared with respect to geometrically different parts. Major manufacturing data have been taken into consideration prior to the tool paths generation to achieve high success rate of manufacturing.

VALIDATING the Accuracy of Sighten's Automated Shading Tool

DOE Office of Scientific and Technical Information (OSTI.GOV)

Solar companies - including installers, financiers, and distributors - leverage Sighten software to deliver accurate shading calculations and solar proposals. Sighten recently partnered with Google Project Sunroof to provide automated remote shading analysis directly within the Sighten platform. The National Renewable Energy Laboratory (NREL), in partnership with Sighten, independently verified the accuracy of Sighten's remote-shading solar access values (SAVs) on an annual basis for locations in Los Angeles, California, and Denver, Colorado.

Automated Source-Code-Based Testing of Object-Oriented Software

NASA Astrophysics Data System (ADS)

Gerlich, Ralf; Gerlich, Rainer; Dietrich, Carsten

2014-08-01

With the advent of languages such as C++ and Java in mission- and safety-critical space on-board software, new challenges for testing and specifically automated testing arise. In this paper we discuss some of these challenges, consequences and solutions based on an experiment in automated source- code-based testing for C++.

HDX Workbench: Software for the Analysis of H/D Exchange MS Data

NASA Astrophysics Data System (ADS)

Pascal, Bruce D.; Willis, Scooter; Lauer, Janelle L.; Landgraf, Rachelle R.; West, Graham M.; Marciano, David; Novick, Scott; Goswami, Devrishi; Chalmers, Michael J.; Griffin, Patrick R.

2012-09-01

Hydrogen/deuterium exchange mass spectrometry (HDX-MS) is an established method for the interrogation of protein conformation and dynamics. While the data analysis challenge of HDX-MS has been addressed by a number of software packages, new computational tools are needed to keep pace with the improved methods and throughput of this technique. To address these needs, we report an integrated desktop program titled HDX Workbench, which facilitates automation, management, visualization, and statistical cross-comparison of large HDX data sets. Using the software, validated data analysis can be achieved at the rate of generation. The application is available at the project home page http://hdx.florida.scripps.edu.

Reliability, Safety and Error Recovery for Advanced Control Software

NASA Technical Reports Server (NTRS)

Malin, Jane T.

2003-01-01

For long-duration automated operation of regenerative life support systems in space environments, there is a need for advanced integration and control systems that are significantly more reliable and safe, and that support error recovery and minimization of operational failures. This presentation outlines some challenges of hazardous space environments and complex system interactions that can lead to system accidents. It discusses approaches to hazard analysis and error recovery for control software and challenges of supporting effective intervention by safety software and the crew.

Continuous integration and quality control for scientific software

NASA Astrophysics Data System (ADS)

Neidhardt, A.; Ettl, M.; Brisken, W.; Dassing, R.

2013-08-01

Modern software has to be stable, portable, fast and reliable. This is going to be also more and more important for scientific software. But this requires a sophisticated way to inspect, check and evaluate the quality of source code with a suitable, automated infrastructure. A centralized server with a software repository and a version control system is one essential part, to manage the code basis and to control the different development versions. While each project can be compiled separately, the whole code basis can also be compiled with one central “Makefile”. This is used to create automated, nightly builds. Additionally all sources are inspected automatically with static code analysis and inspection tools, which check well-none error situations, memory and resource leaks, performance issues, or style issues. In combination with an automatic documentation generator it is possible to create the developer documentation directly from the code and the inline comments. All reports and generated information are presented as HTML page on a Web server. Because this environment increased the stability and quality of the software of the Geodetic Observatory Wettzell tremendously, it is now also available for scientific communities. One regular customer is already the developer group of the DiFX software correlator project.

Orchestrating high-throughput genomic analysis with Bioconductor

PubMed Central

Huber, Wolfgang; Carey, Vincent J.; Gentleman, Robert; Anders, Simon; Carlson, Marc; Carvalho, Benilton S.; Bravo, Hector Corrada; Davis, Sean; Gatto, Laurent; Girke, Thomas; Gottardo, Raphael; Hahne, Florian; Hansen, Kasper D.; Irizarry, Rafael A.; Lawrence, Michael; Love, Michael I.; MacDonald, James; Obenchain, Valerie; Oleś, Andrzej K.; Pagès, Hervé; Reyes, Alejandro; Shannon, Paul; Smyth, Gordon K.; Tenenbaum, Dan; Waldron, Levi; Morgan, Martin

2015-01-01

Bioconductor is an open-source, open-development software project for the analysis and comprehension of high-throughput data in genomics and molecular biology. The project aims to enable interdisciplinary research, collaboration and rapid development of scientific software. Based on the statistical programming language R, Bioconductor comprises 934 interoperable packages contributed by a large, diverse community of scientists. Packages cover a range of bioinformatic and statistical applications. They undergo formal initial review and continuous automated testing. We present an overview for prospective users and contributors. PMID:25633503

Novel semi-automated kidney volume measurements in autosomal dominant polycystic kidney disease.

PubMed

Muto, Satoru; Kawano, Haruna; Isotani, Shuji; Ide, Hisamitsu; Horie, Shigeo

2018-06-01

We assessed the effectiveness and convenience of a novel semi-automatic kidney volume (KV) measuring high-speed 3D-image analysis system SYNAPSE VINCENT ® (Fuji Medical Systems, Tokyo, Japan) for autosomal dominant polycystic kidney disease (ADPKD) patients. We developed a novel semi-automated KV measurement software for patients with ADPKD to be included in the imaging analysis software SYNAPSE VINCENT ® . The software extracts renal regions using image recognition software and measures KV (VINCENT KV). The algorithm was designed to work with the manual designation of a long axis of a kidney including cysts. After using the software to assess the predictive accuracy of the VINCENT method, we performed an external validation study and compared accurate KV and ellipsoid KV based on geometric modeling by linear regression analysis and Bland-Altman analysis. Median eGFR was 46.9 ml/min/1.73 m 2 . Median accurate KV, Vincent KV and ellipsoid KV were 627.7, 619.4 ml (IQR 431.5-947.0) and 694.0 ml (IQR 488.1-1107.4), respectively. Compared with ellipsoid KV (r = 0.9504), Vincent KV correlated strongly with accurate KV (r = 0.9968), without systematic underestimation or overestimation (ellipsoid KV; 14.2 ± 22.0%, Vincent KV; - 0.6 ± 6.0%). There were no significant slice thickness-specific differences (p = 0.2980). The VINCENT method is an accurate and convenient semi-automatic method to measure KV in patients with ADPKD compared with the conventional ellipsoid method.

Development of an automated analysis system for data from flow cytometric intracellular cytokine staining assays from clinical vaccine trials

PubMed Central

Shulman, Nick; Bellew, Matthew; Snelling, George; Carter, Donald; Huang, Yunda; Li, Hongli; Self, Steven G.; McElrath, M. Juliana; De Rosa, Stephen C.

2008-01-01

Background Intracellular cytokine staining (ICS) by multiparameter flow cytometry is one of the primary methods for determining T cell immunogenicity in HIV-1 clinical vaccine trials. Data analysis requires considerable expertise and time. The amount of data is quickly increasing as more and larger trials are performed, and thus there is a critical need for high throughput methods of data analysis. Methods A web based flow cytometric analysis system, LabKey Flow, was developed for analyses of data from standardized ICS assays. A gating template was created manually in commercially-available flow cytometric analysis software. Using this template, the system automatically compensated and analyzed all data sets. Quality control queries were designed to identify potentially incorrect sample collections. Results Comparison of the semi-automated analysis performed by LabKey Flow and the manual analysis performed using FlowJo software demonstrated excellent concordance (concordance correlation coefficient >0.990). Manual inspection of the analyses performed by LabKey Flow for 8-color ICS data files from several clinical vaccine trials indicates that template gates can appropriately be used for most data sets. Conclusions The semi-automated LabKey Flow analysis system can analyze accurately large ICS data files. Routine use of the system does not require specialized expertise. This high-throughput analysis will provide great utility for rapid evaluation of complex multiparameter flow cytometric measurements collected from large clinical trials. PMID:18615598

End-to-end automated microfluidic platform for synthetic biology: from design to functional analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Linshiz, Gregory; Jensen, Erik; Stawski, Nina

Synthetic biology aims to engineer biological systems for desired behaviors. The construction of these systems can be complex, often requiring genetic reprogramming, extensive de novo DNA synthesis, and functional screening. Here, we present a programmable, multipurpose microfluidic platform and associated software and apply the platform to major steps of the synthetic biology research cycle: design, construction, testing, and analysis. We show the platform’s capabilities for multiple automated DNA assembly methods, including a new method for Isothermal Hierarchical DNA Construction, and for Escherichia coli and Saccharomyces cerevisiae transformation. The platform enables the automated control of cellular growth, gene expression induction, andmore » proteogenic and metabolic output analysis. Finally, taken together, we demonstrate the microfluidic platform’s potential to provide end-to-end solutions for synthetic biology research, from design to functional analysis.« less

End-to-end automated microfluidic platform for synthetic biology: from design to functional analysis

DOE PAGES

Linshiz, Gregory; Jensen, Erik; Stawski, Nina; ...

2016-02-02

Synthetic biology aims to engineer biological systems for desired behaviors. The construction of these systems can be complex, often requiring genetic reprogramming, extensive de novo DNA synthesis, and functional screening. Here, we present a programmable, multipurpose microfluidic platform and associated software and apply the platform to major steps of the synthetic biology research cycle: design, construction, testing, and analysis. We show the platform’s capabilities for multiple automated DNA assembly methods, including a new method for Isothermal Hierarchical DNA Construction, and for Escherichia coli and Saccharomyces cerevisiae transformation. The platform enables the automated control of cellular growth, gene expression induction, andmore » proteogenic and metabolic output analysis. Finally, taken together, we demonstrate the microfluidic platform’s potential to provide end-to-end solutions for synthetic biology research, from design to functional analysis.« less

Quantification of diffusion tensor imaging in normal white matter maturation of early childhood using an automated processing pipeline.

PubMed

Loh, K B; Ramli, N; Tan, L K; Roziah, M; Rahmat, K; Ariffin, H

2012-07-01

The degree and status of white matter myelination can be sensitively monitored using diffusion tensor imaging (DTI). This study looks at the measurement of fractional anistropy (FA) and mean diffusivity (MD) using an automated ROI with an existing DTI atlas. Anatomical MRI and structural DTI were performed cross-sectionally on 26 normal children (newborn to 48 months old), using 1.5-T MRI. The automated processing pipeline was implemented to convert diffusion-weighted images into the NIfTI format. DTI-TK software was used to register the processed images to the ICBM DTI-81 atlas, while AFNI software was used for automated atlas-based volumes of interest (VOIs) and statistical value extraction. DTI exhibited consistent grey-white matter contrast. Triphasic temporal variation of the FA and MD values was noted, with FA increasing and MD decreasing rapidly early in the first 12 months. The second phase lasted 12-24 months during which the rate of FA and MD changes was reduced. After 24 months, the FA and MD values plateaued. DTI is a superior technique to conventional MR imaging in depicting WM maturation. The use of the automated processing pipeline provides a reliable environment for quantitative analysis of high-throughput DTI data. Diffusion tensor imaging outperforms conventional MRI in depicting white matter maturation. • DTI will become an important clinical tool for diagnosing paediatric neurological diseases. • DTI appears especially helpful for developmental abnormalities, tumours and white matter disease. • An automated processing pipeline assists quantitative analysis of high throughput DTI data.

Flight flutter testing technology at Grumman. [automated telemetry station for on line data reduction

NASA Technical Reports Server (NTRS)

Perangelo, H. J.; Milordi, F. W.

1976-01-01

Analysis techniques used in the automated telemetry station (ATS) for on line data reduction are encompassed in a broad range of software programs. Concepts that form the basis for the algorithms used are mathematically described. The control the user has in interfacing with various on line programs is discussed. The various programs are applied to an analysis of flight data which includes unimodal and bimodal response signals excited via a swept frequency shaker and/or random aerodynamic forces. A nonlinear response error modeling analysis approach is described. Preliminary results in the analysis of a hard spring nonlinear resonant system are also included.

Rocketdyne automated dynamics data analysis and management system

NASA Technical Reports Server (NTRS)

Tarn, Robert B.

1988-01-01

An automated dynamics data analysis and management systems implemented on a DEC VAX minicomputer cluster is described. Multichannel acquisition, Fast Fourier Transformation analysis, and an online database have significantly improved the analysis of wideband transducer responses from Space Shuttle Main Engine testing. Leakage error correction to recover sinusoid amplitudes and correct for frequency slewing is described. The phase errors caused by FM recorder/playback head misalignment are automatically measured and used to correct the data. Data compression methods are described and compared. The system hardware is described. Applications using the data base are introduced, including software for power spectral density, instantaneous time history, amplitude histogram, fatigue analysis, and rotordynamics expert system analysis.

Program Model Checking as a New Trend

NASA Technical Reports Server (NTRS)

Havelund, Klaus; Visser, Willem; Clancy, Daniel (Technical Monitor)

2002-01-01

This paper introduces a special section of STTT (International Journal on Software Tools for Technology Transfer) containing a selection of papers that were presented at the 7th International SPIN workshop, Stanford, August 30 - September 1, 2000. The workshop was named SPIN Model Checking and Software Verification, with an emphasis on model checking of programs. The paper outlines the motivation for stressing software verification, rather than only design and model verification, by presenting the work done in the Automated Software Engineering group at NASA Ames Research Center within the last 5 years. This includes work in software model checking, testing like technologies and static analysis.

Automated Data Abstraction of Cardiopulmonary Resuscitation Process Measures for Complete Episodes of Cardiac Arrest Resuscitation.

PubMed

Lin, Steve; Turgulov, Anuar; Taher, Ahmed; Buick, Jason E; Byers, Adam; Drennan, Ian R; Hu, Samantha; J Morrison, Laurie

2016-10-01

Cardiopulmonary resuscitation (CPR) process measures research and quality assurance has traditionally been limited to the first 5 minutes of resuscitation due to significant costs in time, resources, and personnel from manual data abstraction. CPR performance may change over time during prolonged resuscitations, which represents a significant knowledge gap. Moreover, currently available commercial software output of CPR process measures are difficult to analyze. The objective was to develop and validate a software program to help automate the abstraction and transfer of CPR process measures data from electronic defibrillators for complete episodes of cardiac arrest resuscitation. We developed a software program to facilitate and help automate CPR data abstraction and transfer from electronic defibrillators for entire resuscitation episodes. Using an intermediary Extensible Markup Language export file, the automated software transfers CPR process measures data (electrocardiogram [ECG] number, CPR start time, number of ventilations, number of chest compressions, compression rate per minute, compression depth per minute, compression fraction, and end-tidal CO 2 per minute). We performed an internal validation of the software program on 50 randomly selected cardiac arrest cases with resuscitation durations between 15 and 60 minutes. CPR process measures were manually abstracted and transferred independently by two trained data abstractors and by the automated software program, followed by manual interpretation of raw ECG tracings, treatment interventions, and patient events. Error rates and the time needed for data abstraction, transfer, and interpretation were measured for both manual and automated methods, compared to an additional independent reviewer. A total of 9,826 data points were each abstracted by the two abstractors and by the software program. Manual data abstraction resulted in a total of six errors (0.06%) compared to zero errors by the software program. The mean ± SD time measured per case for manual data abstraction was 20.3 ± 2.7 minutes compared to 5.3 ± 1.4 minutes using the software program (p = 0.003). We developed and validated an automated software program that efficiently abstracts and transfers CPR process measures data from electronic defibrillators for complete cardiac arrest episodes. This software will enable future cardiac arrest studies and quality assurance programs to evaluate the impact of CPR process measures during prolonged resuscitations. © 2016 by the Society for Academic Emergency Medicine.

Standardizing Activation Analysis: New Software for Photon Activation Analysis

NASA Astrophysics Data System (ADS)

Sun, Z. J.; Wells, D.; Segebade, C.; Green, J.

2011-06-01

Photon Activation Analysis (PAA) of environmental, archaeological and industrial samples requires extensive data analysis that is susceptible to error. For the purpose of saving time, manpower and minimizing error, a computer program was designed, built and implemented using SQL, Access 2007 and asp.net technology to automate this process. Based on the peak information of the spectrum and assisted by its PAA library, the program automatically identifies elements in the samples and calculates their concentrations and respective uncertainties. The software also could be operated in browser/server mode, which gives the possibility to use it anywhere the internet is accessible. By switching the nuclide library and the related formula behind, the new software can be easily expanded to neutron activation analysis (NAA), charged particle activation analysis (CPAA) or proton-induced X-ray emission (PIXE). Implementation of this would standardize the analysis of nuclear activation data. Results from this software were compared to standard PAA analysis with excellent agreement. With minimum input from the user, the software has proven to be fast, user-friendly and reliable.

Clinical Chemistry Laboratory Automation in the 21st Century - Amat Victoria curam (Victory loves careful preparation)

PubMed Central

Armbruster, David A; Overcash, David R; Reyes, Jaime

2014-01-01

The era of automation arrived with the introduction of the AutoAnalyzer using continuous flow analysis and the Robot Chemist that automated the traditional manual analytical steps. Successive generations of stand-alone analysers increased analytical speed, offered the ability to test high volumes of patient specimens, and provided large assay menus. A dichotomy developed, with a group of analysers devoted to performing routine clinical chemistry tests and another group dedicated to performing immunoassays using a variety of methodologies. Development of integrated systems greatly improved the analytical phase of clinical laboratory testing and further automation was developed for pre-analytical procedures, such as sample identification, sorting, and centrifugation, and post-analytical procedures, such as specimen storage and archiving. All phases of testing were ultimately combined in total laboratory automation (TLA) through which all modules involved are physically linked by some kind of track system, moving samples through the process from beginning-to-end. A newer and very powerful, analytical methodology is liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS). LC-MS/MS has been automated but a future automation challenge will be to incorporate LC-MS/MS into TLA configurations. Another important facet of automation is informatics, including middleware, which interfaces the analyser software to a laboratory information systems (LIS) and/or hospital information systems (HIS). This software includes control of the overall operation of a TLA configuration and combines analytical results with patient demographic information to provide additional clinically useful information. This review describes automation relevant to clinical chemistry, but it must be recognised that automation applies to other specialties in the laboratory, e.g. haematology, urinalysis, microbiology. It is a given that automation will continue to evolve in the clinical laboratory, limited only by the imagination and ingenuity of laboratory scientists. PMID:25336760

Clinical Chemistry Laboratory Automation in the 21st Century - Amat Victoria curam (Victory loves careful preparation).

PubMed

Armbruster, David A; Overcash, David R; Reyes, Jaime

2014-08-01

The era of automation arrived with the introduction of the AutoAnalyzer using continuous flow analysis and the Robot Chemist that automated the traditional manual analytical steps. Successive generations of stand-alone analysers increased analytical speed, offered the ability to test high volumes of patient specimens, and provided large assay menus. A dichotomy developed, with a group of analysers devoted to performing routine clinical chemistry tests and another group dedicated to performing immunoassays using a variety of methodologies. Development of integrated systems greatly improved the analytical phase of clinical laboratory testing and further automation was developed for pre-analytical procedures, such as sample identification, sorting, and centrifugation, and post-analytical procedures, such as specimen storage and archiving. All phases of testing were ultimately combined in total laboratory automation (TLA) through which all modules involved are physically linked by some kind of track system, moving samples through the process from beginning-to-end. A newer and very powerful, analytical methodology is liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS). LC-MS/MS has been automated but a future automation challenge will be to incorporate LC-MS/MS into TLA configurations. Another important facet of automation is informatics, including middleware, which interfaces the analyser software to a laboratory information systems (LIS) and/or hospital information systems (HIS). This software includes control of the overall operation of a TLA configuration and combines analytical results with patient demographic information to provide additional clinically useful information. This review describes automation relevant to clinical chemistry, but it must be recognised that automation applies to other specialties in the laboratory, e.g. haematology, urinalysis, microbiology. It is a given that automation will continue to evolve in the clinical laboratory, limited only by the imagination and ingenuity of laboratory scientists.

Automated analysis of angle closure from anterior chamber angle images.

PubMed

Baskaran, Mani; Cheng, Jun; Perera, Shamira A; Tun, Tin A; Liu, Jiang; Aung, Tin

2014-10-21

To evaluate a novel software capable of automatically grading angle closure on EyeCam angle images in comparison with manual grading of images, with gonioscopy as the reference standard. In this hospital-based, prospective study, subjects underwent gonioscopy by a single observer, and EyeCam imaging by a different operator. The anterior chamber angle in a quadrant was classified as closed if the posterior trabecular meshwork could not be seen. An eye was classified as having angle closure if there were two or more quadrants of closure. Automated grading of the angle images was performed using customized software. Agreement between the methods was ascertained by κ statistic and comparison of area under receiver operating characteristic curves (AUC). One hundred forty subjects (140 eyes) were included, most of whom were Chinese (102/140, 72.9%) and women (72/140, 51.5%). Angle closure was detected in 61 eyes (43.6%) with gonioscopy in comparison with 59 eyes (42.1%, P = 0.73) using manual grading, and 67 eyes (47.9%, P = 0.24) with automated grading of EyeCam images. The agreement for angle closure diagnosis between gonioscopy and both manual (κ = 0.88; 95% confidence interval [CI), 0.81-0.96) and automated grading of EyeCam images was good (κ = 0.74; 95% CI, 0.63-0.85). The AUC for detecting eyes with gonioscopic angle closure was comparable for manual and automated grading (AUC 0.974 vs. 0.954, P = 0.31) of EyeCam images. Customized software for automated grading of EyeCam angle images was found to have good agreement with gonioscopy. Human observation of the EyeCam images may still be needed to avoid gross misclassification, especially in eyes with extensive angle closure. Copyright 2014 The Association for Research in Vision and Ophthalmology, Inc.

Clinical Severity Classification using Automated Conjunctival Hyperemia Analysis Software in Patients with Superior Limbic Keratoconjunctivitis.

PubMed

Kurita, Junki; Shoji, Jun; Inada, Noriko; Yoneda, Tsuyoshi; Sumi, Tamaki; Kobayashi, Masahiko; Hoshikawa, Yasuhiro; Fukushima, Atsuki; Yamagami, Satoru

2018-06-01

Digitization of clinical observation is necessary for assessing the severity of superior limbic keratoconjunctivitis (SLK). This study aimed to use a novel quantitative marker to examine hyperemia in patients with SLK. We included six eyes of six patients with both dry eye disease and SLK (SLK group) and eight eyes of eight patients with Sjögren syndrome (SS group). We simultaneously obtained the objective finding scores by using slit-lamp examination and calculated the superior hyperemia index (SHI) with an automated conjunctival hyperemia analysis software by using photographs of the anterior segment. Three objective finding scores, including papillary formation of the superior palpebral conjunctiva, superior limbal hyperemia and swelling, and superior corneal epitheliopathy, were determined. The SHI was calculated as the superior/temporal ratio of bulbar conjunctival hyperemia by using the software. Fisher's exact test was used to compare a high SHI (≥1.07) ratio between the SLK and SS groups. P-Values < 0.05 were considered statistically significant. The SHI (mean ± standard deviation) in the SLK and SS groups was 1.19 ± 0.50 and 0.69 ± 0.24, respectively. The number of patients with a high SHI (≥1.07) was significantly higher in the SLK group than in the SS group (p < 0.05). The sensitivity and specificity of the SHI in the differential diagnosis between SS and SLK were 66.7% and 87.5%, respectively. An analysis of the association between the objective finding scores and SHI showed that the SHI had a tendency to indicate the severity of superior limbal hyperemia and swelling score in the SLK group. The SHI calculated using the automated conjunctival hyperemia analysis software could successfully quantify superior bulbar conjunctival hyperemia and may be a useful tool for the differential diagnosis between SS and SLK and for the quantitative follow-up of patients with SLK.

SPARTA: Simple Program for Automated reference-based bacterial RNA-seq Transcriptome Analysis.

PubMed

Johnson, Benjamin K; Scholz, Matthew B; Teal, Tracy K; Abramovitch, Robert B

2016-02-04

Many tools exist in the analysis of bacterial RNA sequencing (RNA-seq) transcriptional profiling experiments to identify differentially expressed genes between experimental conditions. Generally, the workflow includes quality control of reads, mapping to a reference, counting transcript abundance, and statistical tests for differentially expressed genes. In spite of the numerous tools developed for each component of an RNA-seq analysis workflow, easy-to-use bacterially oriented workflow applications to combine multiple tools and automate the process are lacking. With many tools to choose from for each step, the task of identifying a specific tool, adapting the input/output options to the specific use-case, and integrating the tools into a coherent analysis pipeline is not a trivial endeavor, particularly for microbiologists with limited bioinformatics experience. To make bacterial RNA-seq data analysis more accessible, we developed a Simple Program for Automated reference-based bacterial RNA-seq Transcriptome Analysis (SPARTA). SPARTA is a reference-based bacterial RNA-seq analysis workflow application for single-end Illumina reads. SPARTA is turnkey software that simplifies the process of analyzing RNA-seq data sets, making bacterial RNA-seq analysis a routine process that can be undertaken on a personal computer or in the classroom. The easy-to-install, complete workflow processes whole transcriptome shotgun sequencing data files by trimming reads and removing adapters, mapping reads to a reference, counting gene features, calculating differential gene expression, and, importantly, checking for potential batch effects within the data set. SPARTA outputs quality analysis reports, gene feature counts and differential gene expression tables and scatterplots. SPARTA provides an easy-to-use bacterial RNA-seq transcriptional profiling workflow to identify differentially expressed genes between experimental conditions. This software will enable microbiologists with limited bioinformatics experience to analyze their data and integrate next generation sequencing (NGS) technologies into the classroom. The SPARTA software and tutorial are available at sparta.readthedocs.org.

New technologies for advanced three-dimensional optimum shape design in aeronautics

NASA Astrophysics Data System (ADS)

Dervieux, Alain; Lanteri, Stéphane; Malé, Jean-Michel; Marco, Nathalie; Rostaing-Schmidt, Nicole; Stoufflet, Bruno

1999-05-01

The analysis of complex flows around realistic aircraft geometries is becoming more and more predictive. In order to obtain this result, the complexity of flow analysis codes has been constantly increasing, involving more refined fluid models and sophisticated numerical methods. These codes can only run on top computers, exhausting their memory and CPU capabilities. It is, therefore, difficult to introduce best analysis codes in a shape optimization loop: most previous works in the optimum shape design field used only simplified analysis codes. Moreover, as the most popular optimization methods are the gradient-based ones, the more complex the flow solver, the more difficult it is to compute the sensitivity code. However, emerging technologies are contributing to make such an ambitious project, of including a state-of-the-art flow analysis code into an optimisation loop, feasible. Among those technologies, there are three important issues that this paper wishes to address: shape parametrization, automated differentiation and parallel computing. Shape parametrization allows faster optimization by reducing the number of design variable; in this work, it relies on a hierarchical multilevel approach. The sensitivity code can be obtained using automated differentiation. The automated approach is based on software manipulation tools, which allow the differentiation to be quick and the resulting differentiated code to be rather fast and reliable. In addition, the parallel algorithms implemented in this work allow the resulting optimization software to run on increasingly larger geometries. Copyright

Improvement of Computer Software Quality through Software Automated Tools.

DTIC Science & Technology

1986-08-31

requirement for increased emphasis on software quality assurance has lead to the creation of various methods of verification and validation. Experience...result was a vast array of methods , systems, languages and automated tools to assist in the process. Given that the primary role of quality assurance is...Unfortunately, there is no single method , tool or technique that can insure accurate, reliable and cost effective software. Therefore, government and industry

An automated system for creep testing

NASA Technical Reports Server (NTRS)

Spiegel, F. Xavier; Weigman, Bernard J.

1992-01-01

A completely automated data collection system was devised to measure, analyze, and graph creep versus time using a PC, a 16 channel multiplexed analog to digital converter, and low friction potentiometers to measure length. The sampling rate for each experiment can be adjusted in the software to meet the needs of the material tested. Data is collected and stored on a diskette for permanent record and also for later data analysis on a different machine.

Utility of the summation chromatographic peak integration function to avoid manual reintegrations in the analysis of targeted analytes

USDA-ARS?s Scientific Manuscript database

As sample preparation and analytical techniques have improved, data handling has become the main limitation in automated high-throughput analysis of targeted chemicals in many applications. Conventional chromatographic peak integration functions rely on complex software and settings, but untrustwor...

RootScan: Software for high-throughput analysis of root anatomical traits

USDA-ARS?s Scientific Manuscript database

RootScan is a program for semi-automated image analysis of anatomical phenes in root cross-sections. RootScan uses pixel value thresholds to separate the cross-section from its background and to visually dissect it into tissue regions. Area measurements and object counts are performed within various...

Artificial intelligence in mitral valve analysis.

PubMed

Jeganathan, Jelliffe; Knio, Ziyad; Amador, Yannis; Hai, Ting; Khamooshian, Arash; Matyal, Robina; Khabbaz, Kamal R; Mahmood, Feroze

2017-01-01

Echocardiographic analysis of mitral valve (MV) has become essential for diagnosis and management of patients with MV disease. Currently, the various software used for MV analysis require manual input and are prone to interobserver variability in the measurements. The aim of this study is to determine the interobserver variability in an automated software that uses artificial intelligence for MV analysis. Retrospective analysis of intraoperative three-dimensional transesophageal echocardiography data acquired from four patients with normal MV undergoing coronary artery bypass graft surgery in a tertiary hospital. Echocardiographic data were analyzed using the eSie Valve Software (Siemens Healthcare, Mountain View, CA, USA). Three examiners analyzed three end-systolic (ES) frames from each of the four patients. A total of 36 ES frames were analyzed and included in the study. A multiple mixed-effects ANOVA model was constructed to determine if the examiner, the patient, and the loop had a significant effect on the average value of each parameter. A Bonferroni correction was used to correct for multiple comparisons, and P = 0.0083 was considered to be significant. Examiners did not have an effect on any of the six parameters tested. Patient and loop had an effect on the average parameter value for each of the six parameters as expected (P < 0.0083 for both). We were able to conclude that using automated analysis, it is possible to obtain results with good reproducibility, which only requires minimal user intervention.

Network Meta-Analysis Using R: A Review of Currently Available Automated Packages

PubMed Central

Neupane, Binod; Richer, Danielle; Bonner, Ashley Joel; Kibret, Taddele; Beyene, Joseph

2014-01-01

Network meta-analysis (NMA) – a statistical technique that allows comparison of multiple treatments in the same meta-analysis simultaneously – has become increasingly popular in the medical literature in recent years. The statistical methodology underpinning this technique and software tools for implementing the methods are evolving. Both commercial and freely available statistical software packages have been developed to facilitate the statistical computations using NMA with varying degrees of functionality and ease of use. This paper aims to introduce the reader to three R packages, namely, gemtc, pcnetmeta, and netmeta, which are freely available software tools implemented in R. Each automates the process of performing NMA so that users can perform the analysis with minimal computational effort. We present, compare and contrast the availability and functionality of different important features of NMA in these three packages so that clinical investigators and researchers can determine which R packages to implement depending on their analysis needs. Four summary tables detailing (i) data input and network plotting, (ii) modeling options, (iii) assumption checking and diagnostic testing, and (iv) inference and reporting tools, are provided, along with an analysis of a previously published dataset to illustrate the outputs available from each package. We demonstrate that each of the three packages provides a useful set of tools, and combined provide users with nearly all functionality that might be desired when conducting a NMA. PMID:25541687

Network meta-analysis using R: a review of currently available automated packages.

PubMed

Neupane, Binod; Richer, Danielle; Bonner, Ashley Joel; Kibret, Taddele; Beyene, Joseph

2014-01-01

Network meta-analysis (NMA)--a statistical technique that allows comparison of multiple treatments in the same meta-analysis simultaneously--has become increasingly popular in the medical literature in recent years. The statistical methodology underpinning this technique and software tools for implementing the methods are evolving. Both commercial and freely available statistical software packages have been developed to facilitate the statistical computations using NMA with varying degrees of functionality and ease of use. This paper aims to introduce the reader to three R packages, namely, gemtc, pcnetmeta, and netmeta, which are freely available software tools implemented in R. Each automates the process of performing NMA so that users can perform the analysis with minimal computational effort. We present, compare and contrast the availability and functionality of different important features of NMA in these three packages so that clinical investigators and researchers can determine which R packages to implement depending on their analysis needs. Four summary tables detailing (i) data input and network plotting, (ii) modeling options, (iii) assumption checking and diagnostic testing, and (iv) inference and reporting tools, are provided, along with an analysis of a previously published dataset to illustrate the outputs available from each package. We demonstrate that each of the three packages provides a useful set of tools, and combined provide users with nearly all functionality that might be desired when conducting a NMA.

Automated Software Development Workstation (ASDW)

NASA Technical Reports Server (NTRS)

Fridge, Ernie

1990-01-01

Software development is a serious bottleneck in the construction of complex automated systems. An increase of the reuse of software designs and components has been viewed as a way to relieve this bottleneck. One approach to achieving software reusability is through the development and use of software parts composition systems. A software parts composition system is a software development environment comprised of a parts description language for modeling parts and their interfaces, a catalog of existing parts, a composition editor that aids a user in the specification of a new application from existing parts, and a code generator that takes a specification and generates an implementation of a new application in a target language. The Automated Software Development Workstation (ASDW) is an expert system shell that provides the capabilities required to develop and manipulate these software parts composition systems. The ASDW is now in Beta testing at the Johnson Space Center. Future work centers on responding to user feedback for capability and usability enhancement, expanding the scope of the software lifecycle that is covered, and in providing solutions to handling very large libraries of reusable components.

MVP-CA Methodology for the Expert System Advocate's Advisor (ESAA)

DOT National Transportation Integrated Search

1997-11-01

The Multi-Viewpoint Clustering Analysis (MVP-CA) tool is a semi-automated tool to provide a valuable aid for comprehension, verification, validation, maintenance, integration, and evolution of complex knowledge-based software systems. In this report,...

Computer Administering of the Psychological Investigations: Set-Relational Representation

NASA Astrophysics Data System (ADS)

Yordzhev, Krasimir

Computer administering of a psychological investigation is the computer representation of the entire procedure of psychological assessments - test construction, test implementation, results evaluation, storage and maintenance of the developed database, its statistical processing, analysis and interpretation. A mathematical description of psychological assessment with the aid of personality tests is discussed in this article. The set theory and the relational algebra are used in this description. A relational model of data, needed to design a computer system for automation of certain psychological assessments is given. Some finite sets and relation on them, which are necessary for creating a personality psychological test, are described. The described model could be used to develop real software for computer administering of any psychological test and there is full automation of the whole process: test construction, test implementation, result evaluation, storage of the developed database, statistical implementation, analysis and interpretation. A software project for computer administering personality psychological tests is suggested.

Automated Testing Experience of the Linear Aerospike SR-71 Experiment (LASRE) Controller

NASA Technical Reports Server (NTRS)

Larson, Richard R.

1999-01-01

System controllers must be fail-safe, low cost, flexible to software changes, able to output health and status words, and permit rapid retest qualification. The system controller designed and tested for the aerospike engine program was an attempt to meet these requirements. This paper describes (1) the aerospike controller design, (2) the automated simulation testing techniques, and (3) the real time monitoring data visualization structure. Controller cost was minimized by design of a single-string system that used an off-the-shelf 486 central processing unit (CPU). A linked-list architecture, with states (nodes) defined in a user-friendly state table, accomplished software changes to the controller. Proven to be fail-safe, this system reported the abort cause and automatically reverted to a safe condition for any first failure. A real time simulation and test system automated the software checkout and retest requirements. A program requirement to decode all abort causes in real time during all ground and flight tests assured the safety of flight decisions and the proper execution of mission rules. The design also included health and status words, and provided a real time analysis interpretation for all health and status data.

PolyPhred analysis software for mutation detection from fluorescence-based sequence data.

PubMed

Montgomery, Kate T; Iartchouck, Oleg; Li, Li; Loomis, Stephanie; Obourn, Vanessa; Kucherlapati, Raju

2008-10-01

The ability to search for genetic variants that may be related to human disease is one of the most exciting consequences of the availability of the sequence of the human genome. Large cohorts of individuals exhibiting certain phenotypes can be studied and candidate genes resequenced. However, the challenge of analyzing sequence data from many individuals with accuracy, speed, and economy is great. This unit describes one set of software tools: Phred, Phrap, PolyPhred, and Consed. Coverage includes the advantages and disadvantages of these analysis tools, details for obtaining and using the software, and the results one may expect. The software is being continually updated to permit further automation of mutation analysis. Currently, however, at least some manual review is required if one wishes to identify 100% of the variants in a sample set.

Vehicle management and mission planning systems with shuttle applications

NASA Technical Reports Server (NTRS)

1972-01-01

A preliminary definition of a concept for an automated system is presented that will support the effective management and planning of space shuttle operations. It is called the Vehicle Management and Mission Planning System (VMMPS). In addition to defining the system and its functions, some of the software requirements of the system are identified and a phased and evolutionary method is recommended for software design, development, and implementation. The concept is composed of eight software subsystems supervised by an executive system. These subsystems are mission design and analysis, flight scheduler, launch operations, vehicle operations, payload support operations, crew support, information management, and flight operations support. In addition to presenting the proposed system, a discussion of the evolutionary software development philosophy that the Mission Planning and Analysis Division (MPAD) would propose to use in developing the required supporting software is included. A preliminary software development schedule is also included.

Automated software development workstation

NASA Technical Reports Server (NTRS)

1986-01-01

Engineering software development was automated using an expert system (rule-based) approach. The use of this technology offers benefits not available from current software development and maintenance methodologies. A workstation was built with a library or program data base with methods for browsing the designs stored; a system for graphical specification of designs including a capability for hierarchical refinement and definition in a graphical design system; and an automated code generation capability in FORTRAN. The workstation was then used in a demonstration with examples from an attitude control subsystem design for the space station. Documentation and recommendations are presented.

Accuracy of a remote quantitative image analysis in the whole slide images.

PubMed

Słodkowska, Janina; Markiewicz, Tomasz; Grala, Bartłomiej; Kozłowski, Wojciech; Papierz, Wielisław; Pleskacz, Katarzyna; Murawski, Piotr

2011-03-30

The rationale for choosing a remote quantitative method supporting a diagnostic decision requires some empirical studies and knowledge on scenarios including valid telepathology standards. The tumours of the central nervous system [CNS] are graded on the base of the morphological features and the Ki-67 labelling Index [Ki-67 LI]. Various methods have been applied for Ki-67 LI estimation. Recently we have introduced the Computerized Analysis of Medical Images [CAMI] software for an automated Ki-67 LI counting in the digital images. Aims of our study was to explore the accuracy and reliability of a remote assessment of Ki-67 LI with CAMI software applied to the whole slide images [WSI]. The WSI representing CNS tumours: 18 meningiomas and 10 oligodendrogliomas were stored on the server of the Warsaw University of Technology. The digital copies of entire glass slides were created automatically by the Aperio ScanScope CS with objective 20x or 40x. Aperio's Image Scope software provided functionality for a remote viewing of WSI. The Ki-67 LI assessment was carried on within 2 out of 20 selected fields of view (objective 40x) representing the highest labelling areas in each WSI. The Ki-67 LI counting was performed by 3 various methods: 1) the manual reading in the light microscope - LM, 2) the automated counting with CAMI software on the digital images - DI , and 3) the remote quantitation on the WSIs - as WSI method. The quality of WSIs and technical efficiency of the on-line system were analysed. The comparative statistical analysis was performed for the results obtained by 3 methods of Ki-67 LI counting. The preliminary analysis showed that in 18% of WSI the results of Ki-67 LI differed from those obtained in other 2 methods of counting when the quality of the glass slides was below the standard range. The results of our investigations indicate that the remote automated Ki-67 LI analysis performed with the CAMI algorithm on the whole slide images of meningiomas and oligodendrogliomas could be successfully used as an alternative method to the manual reading as well as to the digital images quantitation with CAMI software. According to our observation a need of a remote supervision/consultation and training for the effective use of remote quantitative analysis of WSI is necessary.

Astronomical data analysis software and systems I; Proceedings of the 1st Annual Conference, Tucson, AZ, Nov. 6-8, 1991

NASA Technical Reports Server (NTRS)

Worrall, Diana M. (Editor); Biemesderfer, Chris (Editor); Barnes, Jeannette (Editor)

1992-01-01

Consideration is given to a definition of a distribution format for X-ray data, the Einstein on-line system, the NASA/IPAC extragalactic database, COBE astronomical databases, Cosmic Background Explorer astronomical databases, the ADAM software environment, the Groningen Image Processing System, search for a common data model for astronomical data analysis systems, deconvolution for real and synthetic apertures, pitfalls in image reconstruction, a direct method for spectral and image restoration, and a discription of a Poisson imagery super resolution algorithm. Also discussed are multivariate statistics on HI and IRAS images, a faint object classification using neural networks, a matched filter for improving SNR of radio maps, automated aperture photometry of CCD images, interactive graphics interpreter, the ROSAT extreme ultra-violet sky survey, a quantitative study of optimal extraction, an automated analysis of spectra, applications of synthetic photometry, an algorithm for extra-solar planet system detection and data reduction facilities for the William Herschel telescope.

An entirely automated method to score DSS-induced colitis in mice by digital image analysis of pathology slides

PubMed Central

Kozlowski, Cleopatra; Jeet, Surinder; Beyer, Joseph; Guerrero, Steve; Lesch, Justin; Wang, Xiaoting; DeVoss, Jason; Diehl, Lauri

2013-01-01

SUMMARY The DSS (dextran sulfate sodium) model of colitis is a mouse model of inflammatory bowel disease. Microscopic symptoms include loss of crypt cells from the gut lining and infiltration of inflammatory cells into the colon. An experienced pathologist requires several hours per study to score histological changes in selected regions of the mouse gut. In order to increase the efficiency of scoring, Definiens Developer software was used to devise an entirely automated method to quantify histological changes in the whole H&E slide. When the algorithm was applied to slides from historical drug-discovery studies, automated scores classified 88% of drug candidates in the same way as pathologists’ scores. In addition, another automated image analysis method was developed to quantify colon-infiltrating macrophages, neutrophils, B cells and T cells in immunohistochemical stains of serial sections of the H&E slides. The timing of neutrophil and macrophage infiltration had the highest correlation to pathological changes, whereas T and B cell infiltration occurred later. Thus, automated image analysis enables quantitative comparisons between tissue morphology changes and cell-infiltration dynamics. PMID:23580198

Automated Coding Software: Development and Use to Enhance Anti-Fraud Activities*

PubMed Central

Garvin, Jennifer H.; Watzlaf, Valerie; Moeini, Sohrab

2006-01-01

This descriptive research project identified characteristics of automated coding systems that have the potential to detect improper coding and to minimize improper or fraudulent coding practices in the setting of automated coding used with the electronic health record (EHR). Recommendations were also developed for software developers and users of coding products to maximize anti-fraud practices. PMID:17238546

Automated Estimation Of Software-Development Costs

NASA Technical Reports Server (NTRS)

Roush, George B.; Reini, William

1993-01-01

COSTMODL is automated software development-estimation tool. Yields significant reduction in risk of cost overruns and failed projects. Accepts description of software product developed and computes estimates of effort required to produce it, calendar schedule required, and distribution of effort and staffing as function of defined set of development life-cycle phases. Written for IBM PC(R)-compatible computers.

Automated mixed traffic transit vehicle microprocessor controller

NASA Technical Reports Server (NTRS)

Marks, R. A.; Cassell, P.; Johnston, A. R.

1981-01-01

An improved Automated Mixed Traffic Vehicle (AMTV) speed control system employing a microprocessor and transistor chopper motor current controller is described and its performance is presented in terms of velocity versus time curves. The on board computer hardware and software systems are described as is the software development system. All of the programming used in this controller was implemented using FORTRAN. This microprocessor controller made possible a number of safety features and improved the comfort associated with starting and shopping. In addition, most of the vehicle's performance characteristics can be altered by simple program parameter changes. A failure analysis of the microprocessor controller was generated and the results are included. Flow diagrams for the speed control algorithms and complete FORTRAN code listings are also included.

Automated Reuse of Scientific Subroutine Libraries through Deductive Synthesis

NASA Technical Reports Server (NTRS)

Lowry, Michael R.; Pressburger, Thomas; VanBaalen, Jeffrey; Roach, Steven

1997-01-01

Systematic software construction offers the potential of elevating software engineering from an art-form to an engineering discipline. The desired result is more predictable software development leading to better quality and more maintainable software. However, the overhead costs associated with the formalisms, mathematics, and methods of systematic software construction have largely precluded their adoption in real-world software development. In fact, many mainstream software development organizations, such as Microsoft, still maintain a predominantly oral culture for software development projects; which is far removed from a formalism-based culture for software development. An exception is the limited domain of safety-critical software, where the high-assuiance inherent in systematic software construction justifies the additional cost. We believe that systematic software construction will only be adopted by mainstream software development organization when the overhead costs have been greatly reduced. Two approaches to cost mitigation are reuse (amortizing costs over many applications) and automation. For the last four years, NASA Ames has funded the Amphion project, whose objective is to automate software reuse through techniques from systematic software construction. In particular, deductive program synthesis (i.e., program extraction from proofs) is used to derive a composition of software components (e.g., subroutines) that correctly implements a specification. The construction of reuse libraries of software components is the standard software engineering solution for improving software development productivity and quality.

Automated Cryocooler Monitor and Control System Software

NASA Technical Reports Server (NTRS)

Britchcliffe, Michael J.; Conroy, Bruce L.; Anderson, Paul E.; Wilson, Ahmad

2011-01-01

This software is used in an automated cryogenic control system developed to monitor and control the operation of small-scale cryocoolers. The system was designed to automate the cryogenically cooled low-noise amplifier system described in "Automated Cryocooler Monitor and Control System" (NPO-47246), NASA Tech Briefs, Vol. 35, No. 5 (May 2011), page 7a. The software contains algorithms necessary to convert non-linear output voltages from the cryogenic diode-type thermometers and vacuum pressure and helium pressure sensors, to temperature and pressure units. The control function algorithms use the monitor data to control the cooler power, vacuum solenoid, vacuum pump, and electrical warm-up heaters. The control algorithms are based on a rule-based system that activates the required device based on the operating mode. The external interface is Web-based. It acts as a Web server, providing pages for monitor, control, and configuration. No client software from the external user is required.

A three-dimensional image processing program for accurate, rapid, and semi-automated segmentation of neuronal somata with dense neurite outgrowth

PubMed Central

Ross, James D.; Cullen, D. Kacy; Harris, James P.; LaPlaca, Michelle C.; DeWeerth, Stephen P.

2015-01-01

Three-dimensional (3-D) image analysis techniques provide a powerful means to rapidly and accurately assess complex morphological and functional interactions between neural cells. Current software-based identification methods of neural cells generally fall into two applications: (1) segmentation of cell nuclei in high-density constructs or (2) tracing of cell neurites in single cell investigations. We have developed novel methodologies to permit the systematic identification of populations of neuronal somata possessing rich morphological detail and dense neurite arborization throughout thick tissue or 3-D in vitro constructs. The image analysis incorporates several novel automated features for the discrimination of neurites and somata by initially classifying features in 2-D and merging these classifications into 3-D objects; the 3-D reconstructions automatically identify and adjust for over and under segmentation errors. Additionally, the platform provides for software-assisted error corrections to further minimize error. These features attain very accurate cell boundary identifications to handle a wide range of morphological complexities. We validated these tools using confocal z-stacks from thick 3-D neural constructs where neuronal somata had varying degrees of neurite arborization and complexity, achieving an accuracy of ≥95%. We demonstrated the robustness of these algorithms in a more complex arena through the automated segmentation of neural cells in ex vivo brain slices. These novel methods surpass previous techniques by improving the robustness and accuracy by: (1) the ability to process neurites and somata, (2) bidirectional segmentation correction, and (3) validation via software-assisted user input. This 3-D image analysis platform provides valuable tools for the unbiased analysis of neural tissue or tissue surrogates within a 3-D context, appropriate for the study of multi-dimensional cell-cell and cell-extracellular matrix interactions. PMID:26257609

Space station data system analysis/architecture study. Task 3: Trade studies, DR-5, volume 1

NASA Technical Reports Server (NTRS)

1985-01-01

The primary objective of Task 3 is to provide additional analysis and insight necessary to support key design/programmatic decision for options quantification and selection for system definition. This includes: (1) the identification of key trade study topics; (2) the definition of a trade study procedure for each topic (issues to be resolved, key inputs, criteria/weighting, methodology); (3) conduct tradeoff and sensitivity analysis; and (4) the review/verification of results within the context of evolving system design and definition. The trade study topics addressed in this volume include space autonomy and function automation, software transportability, system network topology, communications standardization, onboard local area networking, distributed operating system, software configuration management, and the software development environment facility.

Improvement of Computer Software Quality through Software Automated Tools.

DTIC Science & Technology

1986-08-30

information that are returned from the tools to the human user, and the forms in which these outputs are presented. Page 2 of 4 STAGE OF DEVELOPMENT: What... AUTOMIATED SOFTWARE TOOL MONITORING SYSTEM APPENDIX 2 2-1 INTRODUCTION This document and Automated Software Tool Monitoring Program (Appendix 1) are...t Output Output features provide links from the tool to both the human user and the target machine (where applicable). They describe the types

Evaluation of automated decisionmaking methodologies and development of an integrated robotic system simulation, volume 2, part 1. Appendix A: Software documentation

NASA Technical Reports Server (NTRS)

Lowrie, J. W.; Fermelia, A. J.; Haley, D. C.; Gremban, K. D.; Vanbaalen, J.; Walsh, R. W.

1982-01-01

Documentation of the preliminary software developed as a framework for a generalized integrated robotic system simulation is presented. The program structure is composed of three major functions controlled by a program executive. The three major functions are: system definition, analysis tools, and post processing. The system definition function handles user input of system parameters and definition of the manipulator configuration. The analysis tools function handles the computational requirements of the program. The post processing function allows for more detailed study of the results of analysis tool function executions. Also documented is the manipulator joint model software to be used as the basis of the manipulator simulation which will be part of the analysis tools capability.

General Staining and Segmentation Procedures for High Content Imaging and Analysis.

PubMed

Chambers, Kevin M; Mandavilli, Bhaskar S; Dolman, Nick J; Janes, Michael S

2018-01-01

Automated quantitative fluorescence microscopy, also known as high content imaging (HCI), is a rapidly growing analytical approach in cell biology. Because automated image analysis relies heavily on robust demarcation of cells and subcellular regions, reliable methods for labeling cells is a critical component of the HCI workflow. Labeling of cells for image segmentation is typically performed with fluorescent probes that bind DNA for nuclear-based cell demarcation or with those which react with proteins for image analysis based on whole cell staining. These reagents, along with instrument and software settings, play an important role in the successful segmentation of cells in a population for automated and quantitative image analysis. In this chapter, we describe standard procedures for labeling and image segmentation in both live and fixed cell samples. The chapter will also provide troubleshooting guidelines for some of the common problems associated with these aspects of HCI.

Ground penetrating radar survey of pavement thickness on Mn/Road sections : final report

DOT National Transportation Integrated Search

1994-11-01

The research shows that highway speed horn antenna ground penetrating radar equipment and automated analysis software can accurately measure asphalt thickness. To accurately measure concrete and base thickness, lower speed ground coupled equipment al...

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pachuilo, Andrew R; Ragan, Eric; Goodall, John R

Visualization tools can take advantage of multiple coordinated views to support analysis of large, multidimensional data sets. Effective design of such views and layouts can be challenging, but understanding users analysis strategies can inform design improvements. We outline an approach for intelligent design configuration of visualization tools with multiple coordinated views, and we discuss a proposed software framework to support the approach. The proposed software framework could capture and learn from user interaction data to automate new compositions of views and widgets. Such a framework could reduce the time needed for meta analysis of the visualization use and lead tomore » more effective visualization design.« less

Digital PIV (DPIV) Software Analysis System

NASA Technical Reports Server (NTRS)

Blackshire, James L.

1997-01-01

A software package was developed to provide a Digital PIV (DPIV) capability for NASA LaRC. The system provides an automated image capture, test correlation, and autocorrelation analysis capability for the Kodak Megaplus 1.4 digital camera system for PIV measurements. The package includes three separate programs that, when used together with the PIV data validation algorithm, constitutes a complete DPIV analysis capability. The programs are run on an IBM PC/AT host computer running either Microsoft Windows 3.1 or Windows 95 using a 'quickwin' format that allows simple user interface and output capabilities to the windows environment.

Automated Analysis of Fluorescence Microscopy Images to Identify Protein-Protein Interactions

DOE PAGES

Venkatraman, S.; Doktycz, M. J.; Qi, H.; ...

2006-01-01

The identification of protein interactions is important for elucidating biological networks. One obstacle in comprehensive interaction studies is the analyses of large datasets, particularly those containing images. Development of an automated system to analyze an image-based protein interaction dataset is needed. Such an analysis system is described here, to automatically extract features from fluorescence microscopy images obtained from a bacterial protein interaction assay. These features are used to relay quantitative values that aid in the automated scoring of positive interactions. Experimental observations indicate that identifying at least 50% positive cells in an image is sufficient to detect a protein interaction.more » Based on this criterion, the automated system presents 100% accuracy in detecting positive interactions for a dataset of 16 images. Algorithms were implemented using MATLAB and the software developed is available on request from the authors.« less

RootGraph: a graphic optimization tool for automated image analysis of plant roots

PubMed Central

Cai, Jinhai; Zeng, Zhanghui; Connor, Jason N.; Huang, Chun Yuan; Melino, Vanessa; Kumar, Pankaj; Miklavcic, Stanley J.

2015-01-01

This paper outlines a numerical scheme for accurate, detailed, and high-throughput image analysis of plant roots. In contrast to existing root image analysis tools that focus on root system-average traits, a novel, fully automated and robust approach for the detailed characterization of root traits, based on a graph optimization process is presented. The scheme, firstly, distinguishes primary roots from lateral roots and, secondly, quantifies a broad spectrum of root traits for each identified primary and lateral root. Thirdly, it associates lateral roots and their properties with the specific primary root from which the laterals emerge. The performance of this approach was evaluated through comparisons with other automated and semi-automated software solutions as well as against results based on manual measurements. The comparisons and subsequent application of the algorithm to an array of experimental data demonstrate that this method outperforms existing methods in terms of accuracy, robustness, and the ability to process root images under high-throughput conditions. PMID:26224880

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sun, Z. J.; Wells, D.; Green, J.

Photon Activation Analysis (PAA) of environmental, archaeological and industrial samples requires extensive data analysis that is susceptible to error. For the purpose of saving time, manpower and minimizing error, a computer program was designed, built and implemented using SQL, Access 2007 and asp.net technology to automate this process. Based on the peak information of the spectrum and assisted by its PAA library, the program automatically identifies elements in the samples and calculates their concentrations and respective uncertainties. The software also could be operated in browser/server mode, which gives the possibility to use it anywhere the internet is accessible. By switchingmore » the nuclide library and the related formula behind, the new software can be easily expanded to neutron activation analysis (NAA), charged particle activation analysis (CPAA) or proton-induced X-ray emission (PIXE). Implementation of this would standardize the analysis of nuclear activation data. Results from this software were compared to standard PAA analysis with excellent agreement. With minimum input from the user, the software has proven to be fast, user-friendly and reliable.« less

A Graphical User Interface for Software-assisted Tracking of Protein Concentration in Dynamic Cellular Protrusions.

PubMed

Saha, Tanumoy; Rathmann, Isabel; Galic, Milos

2017-07-11

Filopodia are dynamic, finger-like cellular protrusions associated with migration and cell-cell communication. In order to better understand the complex signaling mechanisms underlying filopodial initiation, elongation and subsequent stabilization or retraction, it is crucial to determine the spatio-temporal protein activity in these dynamic structures. To analyze protein function in filopodia, we recently developed a semi-automated tracking algorithm that adapts to filopodial shape-changes, thus allowing parallel analysis of protrusion dynamics and relative protein concentration along the whole filopodial length. Here, we present a detailed step-by-step protocol for optimized cell handling, image acquisition and software analysis. We further provide instructions for the use of optional features during image analysis and data representation, as well as troubleshooting guidelines for all critical steps along the way. Finally, we also include a comparison of the described image analysis software with other programs available for filopodia quantification. Together, the presented protocol provides a framework for accurate analysis of protein dynamics in filopodial protrusions using image analysis software.

Three-Dimensional Echocardiographic Assessment of Left Heart Chamber Size and Function with Fully Automated Quantification Software in Patients with Atrial Fibrillation.

PubMed

Otani, Kyoko; Nakazono, Akemi; Salgo, Ivan S; Lang, Roberto M; Takeuchi, Masaaki

2016-10-01

Echocardiographic determination of left heart chamber volumetric parameters by using manual tracings during multiple beats is tedious in atrial fibrillation (AF). The aim of this study was to determine the usefulness of fully automated left chamber quantification software with single-beat three-dimensional transthoracic echocardiographic data sets in patients with AF. Single-beat full-volume three-dimensional transthoracic echocardiographic data sets were prospectively acquired during consecutive multiple cardiac beats (≥10 beats) in 88 patients with AF. In protocol 1, left ventricular volumes, left ventricular ejection fraction, and maximal left atrial volume were validated using automated quantification against the manual tracing method in identical beats in 10 patients. In protocol 2, automated quantification-derived averaged values from multiple beats were compared with the corresponding values obtained from the indexed beat in all patients. Excellent correlations of left chamber parameters between automated quantification and the manual method were observed (r = 0.88-0.98) in protocol 1. The time required for the analysis with the automated quantification method (5 min) was significantly less compared with the manual method (27 min) (P < .0001). In protocol 2, there were excellent linear correlations between the averaged left chamber parameters and the corresponding values obtained from the indexed beat (r = 0.94-0.99), and test-retest variability of left chamber parameters was low (3.5%-4.8%). Three-dimensional transthoracic echocardiography with fully automated quantification software is a rapid and reliable way to measure averaged values of left heart chamber parameters during multiple consecutive beats. Thus, it is a potential new approach for left chamber quantification in patients with AF in daily routine practice. Copyright © 2016 American Society of Echocardiography. Published by Elsevier Inc. All rights reserved.

Performance evaluation of the RITG148+ set of TomoTherapy quality assurance tools using RTQA2 radiochromic film.

PubMed

Lobb, Eric C

2016-07-08

Version 6.3 of the RITG148+ software package offers eight automated analysis routines for quality assurance of the TomoTherapy platform. A performance evaluation of each routine was performed in order to compare RITG148+ results with traditionally accepted analysis techniques and verify that simulated changes in machine parameters are correctly identified by the software. Reference films were exposed according to AAPM TG-148 methodology for each routine and the RITG148+ results were compared with either alternative software analysis techniques or manual analysis techniques in order to assess baseline agreement. Changes in machine performance were simulated through translational and rotational adjustments to subsequently irradiated films, and these films were analyzed to verify that the applied changes were accurately detected by each of the RITG148+ routines. For the Hounsfield unit routine, an assessment of the "Frame Averaging" functionality and the effects of phantom roll on the routine results are presented. All RITG148+ routines reported acceptable baseline results consistent with alternative analysis techniques, with 9 of the 11 baseline test results showing agreement of 0.1mm/0.1° or better. Simulated changes were correctly identified by the RITG148+ routines within approximately 0.2 mm/0.2° with the exception of the Field Centervs. Jaw Setting routine, which was found to have limited accuracy in cases where field centers were not aligned for all jaw settings due to inaccurate autorotation of the film during analysis. The performance of the RITG148+ software package was found to be acceptable for introduction into our clinical environment as an automated alternative to traditional analysis techniques for routine TomoTherapy quality assurance testing.

SamuROI, a Python-Based Software Tool for Visualization and Analysis of Dynamic Time Series Imaging at Multiple Spatial Scales.

PubMed

Rueckl, Martin; Lenzi, Stephen C; Moreno-Velasquez, Laura; Parthier, Daniel; Schmitz, Dietmar; Ruediger, Sten; Johenning, Friedrich W

2017-01-01

The measurement of activity in vivo and in vitro has shifted from electrical to optical methods. While the indicators for imaging activity have improved significantly over the last decade, tools for analysing optical data have not kept pace. Most available analysis tools are limited in their flexibility and applicability to datasets obtained at different spatial scales. Here, we present SamuROI (Structured analysis of multiple user-defined ROIs), an open source Python-based analysis environment for imaging data. SamuROI simplifies exploratory analysis and visualization of image series of fluorescence changes in complex structures over time and is readily applicable at different spatial scales. In this paper, we show the utility of SamuROI in Ca 2+ -imaging based applications at three spatial scales: the micro-scale (i.e., sub-cellular compartments including cell bodies, dendrites and spines); the meso-scale, (i.e., whole cell and population imaging with single-cell resolution); and the macro-scale (i.e., imaging of changes in bulk fluorescence in large brain areas, without cellular resolution). The software described here provides a graphical user interface for intuitive data exploration and region of interest (ROI) management that can be used interactively within Jupyter Notebook: a publicly available interactive Python platform that allows simple integration of our software with existing tools for automated ROI generation and post-processing, as well as custom analysis pipelines. SamuROI software, source code and installation instructions are publicly available on GitHub and documentation is available online. SamuROI reduces the energy barrier for manual exploration and semi-automated analysis of spatially complex Ca 2+ imaging datasets, particularly when these have been acquired at different spatial scales.

SamuROI, a Python-Based Software Tool for Visualization and Analysis of Dynamic Time Series Imaging at Multiple Spatial Scales

PubMed Central

Rueckl, Martin; Lenzi, Stephen C.; Moreno-Velasquez, Laura; Parthier, Daniel; Schmitz, Dietmar; Ruediger, Sten; Johenning, Friedrich W.

2017-01-01

The measurement of activity in vivo and in vitro has shifted from electrical to optical methods. While the indicators for imaging activity have improved significantly over the last decade, tools for analysing optical data have not kept pace. Most available analysis tools are limited in their flexibility and applicability to datasets obtained at different spatial scales. Here, we present SamuROI (Structured analysis of multiple user-defined ROIs), an open source Python-based analysis environment for imaging data. SamuROI simplifies exploratory analysis and visualization of image series of fluorescence changes in complex structures over time and is readily applicable at different spatial scales. In this paper, we show the utility of SamuROI in Ca2+-imaging based applications at three spatial scales: the micro-scale (i.e., sub-cellular compartments including cell bodies, dendrites and spines); the meso-scale, (i.e., whole cell and population imaging with single-cell resolution); and the macro-scale (i.e., imaging of changes in bulk fluorescence in large brain areas, without cellular resolution). The software described here provides a graphical user interface for intuitive data exploration and region of interest (ROI) management that can be used interactively within Jupyter Notebook: a publicly available interactive Python platform that allows simple integration of our software with existing tools for automated ROI generation and post-processing, as well as custom analysis pipelines. SamuROI software, source code and installation instructions are publicly available on GitHub and documentation is available online. SamuROI reduces the energy barrier for manual exploration and semi-automated analysis of spatially complex Ca2+ imaging datasets, particularly when these have been acquired at different spatial scales. PMID:28706482

Automated software for analysis of ciliary beat frequency and metachronal wave orientation in primary ciliary dyskinesia.

PubMed

Mantovani, Giulia; Pifferi, Massimo; Vozzi, Giovanni

2010-06-01

Patients with primary ciliary dyskinesia (PCD) have structural and/or functional alterations of cilia that imply deficits in mucociliary clearance and different respiratory pathologies. A useful indicator for the difficult diagnosis is the ciliary beat frequency (CBF) that is significantly lower in pathological cases than in physiological ones. The CBF computation is not rapid, therefore, the aim of this study is to propose an automated method to evaluate it directly from videos of ciliated cells. The cells are taken from inferior nasal turbinates and videos of ciliary movements are registered and eventually processed by the developed software. The software consists in the extraction of features from videos (written with C++ language) and the computation of the frequency (written with Matlab language). This system was tested both on the samples of nasal cavity and software models, and the results were really promising because in a few seconds, it can compute a reliable frequency if compared with that measured with visual methods. It is to be noticed that the reliability of the computation increases with the quality of acquisition system and especially with the sampling frequency. It is concluded that the developed software could be a useful mean for PCD diagnosis.

Executive system software design and expert system implementation

NASA Technical Reports Server (NTRS)

Allen, Cheryl L.

1992-01-01

The topics are presented in viewgraph form and include: software requirements; design layout of the automated assembly system; menu display for automated composite command; expert system features; complete robot arm state diagram and logic; and expert system benefits.

ROBOCAL: Gamma-ray isotopic hardware/software interface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hurd, J.R.; Bonner, C.A.; Ostenak, C.A.

1989-01-01

ROBOCAL, presently being developed at the Los Alamos National Laboratory, is a full-scale prototypical robotic system for remotely performing calorimetric and gamma-ray isotopics measurements of nuclear materials. It features a fully automated vertical stacker-retriever for storing and retrieving packaged nuclear materials from a multi-drawer system, and a fully automated, uniquely integrated gantry robot for programmable selection and transfer of nuclear materials to calorimetric and gamma-ray isotopic measurement stations. Since ROBOCAL is to require almost no operator intervention, a mechanical control system is required in addition to a totally automated assay system. The assay system must be a completely integrated datamore » acquisition and isotopic analysis package fully capable of performing state-of-the-art homogeneous and heterogeneous analyses on many varied matrices. The TRIFID assay system being discussed at this conference by J. G. Fleissner of the Rocky Flats Plant has been adopted because of its many automated features. These include: MCA/ADC setup and acquisition; spectral storage and analysis utilizing an expert system formalism; report generation with internal measurement control printout; user friendly screens and menus. The mechanical control portion consists primarily of two detector platforms and a sample platform, each with independent movement. Some minor modifications and additions are needed with TRIFID to interface the assay and mechanical portions with the CimRoc 4000 software controlling the robot. 6 refs., 5 figs., 3 tabs.« less

The environmental control and life support system advanced automation project

NASA Technical Reports Server (NTRS)

Dewberry, Brandon S.

1991-01-01

The objective of the ECLSS Advanced Automation project includes reduction of the risk associated with the integration of new, beneficial software techniques. Demonstrations of this software to baseline engineering and test personnel will show the benefits of these techniques. The advanced software will be integrated into ground testing and ground support facilities, familiarizing its usage by key personnel.

Model-Based GN and C Simulation and Flight Software Development for Orion Missions beyond LEO

NASA Technical Reports Server (NTRS)

Odegard, Ryan; Milenkovic, Zoran; Henry, Joel; Buttacoli, Michael

2014-01-01

For Orion missions beyond low Earth orbit (LEO), the Guidance, Navigation, and Control (GN&C) system is being developed using a model-based approach for simulation and flight software. Lessons learned from the development of GN&C algorithms and flight software for the Orion Exploration Flight Test One (EFT-1) vehicle have been applied to the development of further capabilities for Orion GN&C beyond EFT-1. Continuing the use of a Model-Based Development (MBD) approach with the Matlab®/Simulink® tool suite, the process for GN&C development and analysis has been largely improved. Furthermore, a model-based simulation environment in Simulink, rather than an external C-based simulation, greatly eases the process for development of flight algorithms. The benefits seen by employing lessons learned from EFT-1 are described, as well as the approach for implementing additional MBD techniques. Also detailed are the key enablers for improvements to the MBD process, including enhanced configuration management techniques for model-based software systems, automated code and artifact generation, and automated testing and integration.

Automating data analysis for two-dimensional gas chromatography/time-of-flight mass spectrometry non-targeted analysis of comparative samples.

PubMed

Titaley, Ivan A; Ogba, O Maduka; Chibwe, Leah; Hoh, Eunha; Cheong, Paul H-Y; Simonich, Staci L Massey

2018-03-16

Non-targeted analysis of environmental samples, using comprehensive two-dimensional gas chromatography coupled with time-of-flight mass spectrometry (GC × GC/ToF-MS), poses significant data analysis challenges due to the large number of possible analytes. Non-targeted data analysis of complex mixtures is prone to human bias and is laborious, particularly for comparative environmental samples such as contaminated soil pre- and post-bioremediation. To address this research bottleneck, we developed OCTpy, a Python™ script that acts as a data reduction filter to automate GC × GC/ToF-MS data analysis from LECO ® ChromaTOF ® software and facilitates selection of analytes of interest based on peak area comparison between comparative samples. We used data from polycyclic aromatic hydrocarbon (PAH) contaminated soil, pre- and post-bioremediation, to assess the effectiveness of OCTpy in facilitating the selection of analytes that have formed or degraded following treatment. Using datasets from the soil extracts pre- and post-bioremediation, OCTpy selected, on average, 18% of the initial suggested analytes generated by the LECO ® ChromaTOF ® software Statistical Compare feature. Based on this list, 63-100% of the candidate analytes identified by a highly trained individual were also selected by OCTpy. This process was accomplished in several minutes per sample, whereas manual data analysis took several hours per sample. OCTpy automates the analysis of complex mixtures of comparative samples, reduces the potential for human error during heavy data handling and decreases data analysis time by at least tenfold. Copyright © 2018 Elsevier B.V. All rights reserved.

Automated water analyser computer supported system (AWACSS) Part I: Project objectives, basic technology, immunoassay development, software design and networking.

PubMed

Tschmelak, Jens; Proll, Guenther; Riedt, Johannes; Kaiser, Joachim; Kraemmer, Peter; Bárzaga, Luis; Wilkinson, James S; Hua, Ping; Hole, J Patrick; Nudd, Richard; Jackson, Michael; Abuknesha, Ram; Barceló, Damià; Rodriguez-Mozaz, Sara; de Alda, Maria J López; Sacher, Frank; Stien, Jan; Slobodník, Jaroslav; Oswald, Peter; Kozmenko, Helena; Korenková, Eva; Tóthová, Lívia; Krascsenits, Zoltan; Gauglitz, Guenter

2005-02-15

A novel analytical system AWACSS (automated water analyser computer-supported system) based on immunochemical technology has been developed that can measure several organic pollutants at low nanogram per litre level in a single few-minutes analysis without any prior sample pre-concentration nor pre-treatment steps. Having in mind actual needs of water-sector managers related to the implementation of the Drinking Water Directive (DWD) (98/83/EC, 1998) and Water Framework Directive WFD (2000/60/EC, 2000), drinking, ground, surface, and waste waters were major media used for the evaluation of the system performance. The instrument was equipped with remote control and surveillance facilities. The system's software allows for the internet-based networking between the measurement and control stations, global management, trend analysis, and early-warning applications. The experience of water laboratories has been utilised at the design of the instrument's hardware and software in order to make the system rugged and user-friendly. Several market surveys were conducted during the project to assess the applicability of the final system. A web-based AWACSS database was created for automated evaluation and storage of the obtained data in a format compatible with major databases of environmental organic pollutants in Europe. This first part article gives the reader an overview of the aims and scope of the AWACSS project as well as details about basic technology, immunoassays, software, and networking developed and utilised within the research project. The second part article reports on the system performance, first real sample measurements, and an international collaborative trial (inter-laboratory tests) to compare the biosensor with conventional anayltical methods.

Software for rapid time dependent ChIP-sequencing analysis (TDCA).

PubMed

Myschyshyn, Mike; Farren-Dai, Marco; Chuang, Tien-Jui; Vocadlo, David

2017-11-25

Chromatin immunoprecipitation followed by DNA sequencing (ChIP-seq) and associated methods are widely used to define the genome wide distribution of chromatin associated proteins, post-translational epigenetic marks, and modifications found on DNA bases. An area of emerging interest is to study time dependent changes in the distribution of such proteins and marks by using serial ChIP-seq experiments performed in a time resolved manner. Despite such time resolved studies becoming increasingly common, software to facilitate analysis of such data in a robust automated manner is limited. We have designed software called Time-Dependent ChIP-Sequencing Analyser (TDCA), which is the first program to automate analysis of time-dependent ChIP-seq data by fitting to sigmoidal curves. We provide users with guidance for experimental design of TDCA for modeling of time course (TC) ChIP-seq data using two simulated data sets. Furthermore, we demonstrate that this fitting strategy is widely applicable by showing that automated analysis of three previously published TC data sets accurately recapitulates key findings reported in these studies. Using each of these data sets, we highlight how biologically relevant findings can be readily obtained by exploiting TDCA to yield intuitive parameters that describe behavior at either a single locus or sets of loci. TDCA enables customizable analysis of user input aligned DNA sequencing data, coupled with graphical outputs in the form of publication-ready figures that describe behavior at either individual loci or sets of loci sharing common traits defined by the user. TDCA accepts sequencing data as standard binary alignment map (BAM) files and loci of interest in browser extensible data (BED) file format. TDCA accurately models the number of sequencing reads, or coverage, at loci from TC ChIP-seq studies or conceptually related TC sequencing experiments. TC experiments are reduced to intuitive parametric values that facilitate biologically relevant data analysis, and the uncovering of variations in the time-dependent behavior of chromatin. TDCA automates the analysis of TC ChIP-seq experiments, permitting researchers to easily obtain raw and modeled data for specific loci or groups of loci with similar behavior while also enhancing consistency of data analysis of TC data within the genomics field.

Conceptual design of the CZMIL data processing system (DPS): algorithms and software for fusing lidar, hyperspectral data, and digital images

NASA Astrophysics Data System (ADS)

Park, Joong Yong; Tuell, Grady

2010-04-01

The Data Processing System (DPS) of the Coastal Zone Mapping and Imaging Lidar (CZMIL) has been designed to automatically produce a number of novel environmental products through the fusion of Lidar, spectrometer, and camera data in a single software package. These new products significantly transcend use of the system as a bathymeter, and support use of CZMIL as a complete coastal and benthic mapping tool. The DPS provides a spinning globe capability for accessing data files; automated generation of combined topographic and bathymetric point clouds; a fully-integrated manual editor and data analysis tool; automated generation of orthophoto mosaics; automated generation of reflectance data cubes from the imaging spectrometer; a coupled air-ocean spectral optimization model producing images of chlorophyll and CDOM concentrations; and a fusion based capability to produce images and classifications of the shallow water seafloor. Adopting a multitasking approach, we expect to achieve computation of the point clouds, DEMs, and reflectance images at a 1:1 processing to acquisition ratio.

Computer system for scanning tunneling microscope automation

NASA Astrophysics Data System (ADS)

Aguilar, M.; García, A.; Pascual, P. J.; Presa, J.; Santisteban, A.

1987-03-01

A computerized system for the automation of a scanning tunneling microscope is presented. It is based on an IBM personal computer (PC) either an XT or an AT, which performs the control, data acquisition and storage operations, displays the STM "images" in real time, and provides image processing tools for the restoration and analysis of data. It supports different data acquisition and control cards and image display cards. The software has been designed in a modular way to allow the replacement of these cards and other equipment improvements as well as the inclusion of user routines for data analysis.

Solar Asset Management Software

DOE Office of Scientific and Technical Information (OSTI.GOV)

Iverson, Aaron; Zviagin, George

Ra Power Management (RPM) has developed a cloud based software platform that manages the financial and operational functions of third party financed solar projects throughout their lifecycle. RPM’s software streamlines and automates the sales, financing, and management of a portfolio of solar assets. The software helps solar developers automate the most difficult aspects of asset management, leading to increased transparency, efficiency, and reduction in human error. More importantly, our platform will help developers save money by improving their operating margins.

Automating the evaluation of flood damages: methodology and potential gains

NASA Astrophysics Data System (ADS)

Eleutério, Julian; Martinez, Edgar Daniel

2010-05-01

The evaluation of flood damage potential consists of three main steps: assessing and processing data, combining data and calculating potential damages. The first step consists of modelling hazard and assessing vulnerability. In general, this step of the evaluation demands more time and investments than the others. The second step of the evaluation consists of combining spatial data on hazard with spatial data on vulnerability. Geographic Information System (GIS) is a fundamental tool in the realization of this step. GIS software allows the simultaneous analysis of spatial and matrix data. The third step of the evaluation consists of calculating potential damages by means of damage-functions or contingent analysis. All steps demand time and expertise. However, the last two steps must be realized several times when comparing different management scenarios. In addition, uncertainty analysis and sensitivity test are made during the second and third steps of the evaluation. The feasibility of these steps could be relevant in the choice of the extent of the evaluation. Low feasibility could lead to choosing not to evaluate uncertainty or to limit the number of scenario comparisons. Several computer models have been developed over time in order to evaluate the flood risk. GIS software is largely used to realise flood risk analysis. The software is used to combine and process different types of data, and to visualise the risk and the evaluation results. The main advantages of using a GIS in these analyses are: the possibility of "easily" realising the analyses several times, in order to compare different scenarios and study uncertainty; the generation of datasets which could be used any time in future to support territorial decision making; the possibility of adding information over time to update the dataset and make other analyses. However, these analyses require personnel specialisation and time. The use of GIS software to evaluate the flood risk requires personnel with a double professional specialisation. The professional should be proficient in GIS software and in flood damage analysis (which is already a multidisciplinary field). Great effort is necessary in order to correctly evaluate flood damages, and the updating and the improvement of the evaluation over time become a difficult task. The automation of this process should bring great advance in flood management studies over time, especially for public utilities. This study has two specific objectives: (1) show the entire process of automation of the second and third steps of flood damage evaluations; and (2) analyse the induced potential gains in terms of time and expertise needed in the analysis. A programming language is used within GIS software in order to automate hazard and vulnerability data combination and potential damages calculation. We discuss the overall process of flood damage evaluation. The main result of this study is a computational tool which allows significant operational gains on flood loss analyses. We quantify these gains by means of a hypothetical example. The tool significantly reduces the time of analysis and the needs for expertise. An indirect gain is that sensitivity and cost-benefit analyses can be more easily realized.

SPICODYN: A Toolbox for the Analysis of Neuronal Network Dynamics and Connectivity from Multi-Site Spike Signal Recordings.

PubMed

Pastore, Vito Paolo; Godjoski, Aleksandar; Martinoia, Sergio; Massobrio, Paolo

2018-01-01

We implemented an automated and efficient open-source software for the analysis of multi-site neuronal spike signals. The software package, named SPICODYN, has been developed as a standalone windows GUI application, using C# programming language with Microsoft Visual Studio based on .NET framework 4.5 development environment. Accepted input data formats are HDF5, level 5 MAT and text files, containing recorded or generated time series spike signals data. SPICODYN processes such electrophysiological signals focusing on: spiking and bursting dynamics and functional-effective connectivity analysis. In particular, for inferring network connectivity, a new implementation of the transfer entropy method is presented dealing with multiple time delays (temporal extension) and with multiple binary patterns (high order extension). SPICODYN is specifically tailored to process data coming from different Multi-Electrode Arrays setups, guarantying, in those specific cases, automated processing. The optimized implementation of the Delayed Transfer Entropy and the High-Order Transfer Entropy algorithms, allows performing accurate and rapid analysis on multiple spike trains from thousands of electrodes.

Automated Detection of Events of Scientific Interest

NASA Technical Reports Server (NTRS)

James, Mark

2007-01-01

A report presents a slightly different perspective of the subject matter of Fusing Symbolic and Numerical Diagnostic Computations (NPO-42512), which appears elsewhere in this issue of NASA Tech Briefs. Briefly, the subject matter is the X-2000 Anomaly Detection Language, which is a developmental computing language for fusing two diagnostic computer programs one implementing a numerical analysis method, the other implementing a symbolic analysis method into a unified event-based decision analysis software system for real-time detection of events. In the case of the cited companion NASA Tech Briefs article, the contemplated events that one seeks to detect would be primarily failures or other changes that could adversely affect the safety or success of a spacecraft mission. In the case of the instant report, the events to be detected could also include natural phenomena that could be of scientific interest. Hence, the use of X- 2000 Anomaly Detection Language could contribute to a capability for automated, coordinated use of multiple sensors and sensor-output-data-processing hardware and software to effect opportunistic collection and analysis of scientific data.

Artificial Intelligence in Mitral Valve Analysis

PubMed Central

Jeganathan, Jelliffe; Knio, Ziyad; Amador, Yannis; Hai, Ting; Khamooshian, Arash; Matyal, Robina; Khabbaz, Kamal R; Mahmood, Feroze

2017-01-01

Background: Echocardiographic analysis of mitral valve (MV) has become essential for diagnosis and management of patients with MV disease. Currently, the various software used for MV analysis require manual input and are prone to interobserver variability in the measurements. Aim: The aim of this study is to determine the interobserver variability in an automated software that uses artificial intelligence for MV analysis. Settings and Design: Retrospective analysis of intraoperative three-dimensional transesophageal echocardiography data acquired from four patients with normal MV undergoing coronary artery bypass graft surgery in a tertiary hospital. Materials and Methods: Echocardiographic data were analyzed using the eSie Valve Software (Siemens Healthcare, Mountain View, CA, USA). Three examiners analyzed three end-systolic (ES) frames from each of the four patients. A total of 36 ES frames were analyzed and included in the study. Statistical Analysis: A multiple mixed-effects ANOVA model was constructed to determine if the examiner, the patient, and the loop had a significant effect on the average value of each parameter. A Bonferroni correction was used to correct for multiple comparisons, and P = 0.0083 was considered to be significant. Results: Examiners did not have an effect on any of the six parameters tested. Patient and loop had an effect on the average parameter value for each of the six parameters as expected (P < 0.0083 for both). Conclusion: We were able to conclude that using automated analysis, it is possible to obtain results with good reproducibility, which only requires minimal user intervention. PMID:28393769

Exploring the Use of a Test Automation Framework

NASA Technical Reports Server (NTRS)

Cervantes, Alex

2009-01-01

It is known that software testers, more often than not, lack the time needed to fully test the delivered software product within the time period allotted to them. When problems in the implementation phase of a development project occur, it normally causes the software delivery date to slide. As a result, testers either need to work longer hours, or supplementary resources need to be added to the test team in order to meet aggressive test deadlines. One solution to this problem is to provide testers with a test automation framework to facilitate the development of automated test solutions.

Automated diabetic retinopathy detection in smartphone-based fundus photography using artificial intelligence.

PubMed

Rajalakshmi, Ramachandran; Subashini, Radhakrishnan; Anjana, Ranjit Mohan; Mohan, Viswanathan

2018-06-01

To assess the role of artificial intelligence (AI)-based automated software for detection of diabetic retinopathy (DR) and sight-threatening DR (STDR) by fundus photography taken using a smartphone-based device and validate it against ophthalmologist's grading. Three hundred and one patients with type 2 diabetes underwent retinal photography with Remidio 'Fundus on phone' (FOP), a smartphone-based device, at a tertiary care diabetes centre in India. Grading of DR was performed by the ophthalmologists using International Clinical DR (ICDR) classification scale. STDR was defined by the presence of severe non-proliferative DR, proliferative DR or diabetic macular oedema (DME). The retinal photographs were graded using a validated AI DR screening software (EyeArt TM ) designed to identify DR, referable DR (moderate non-proliferative DR or worse and/or DME) or STDR. The sensitivity and specificity of automated grading were assessed and validated against the ophthalmologists' grading. Retinal images of 296 patients were graded. DR was detected by the ophthalmologists in 191 (64.5%) and by the AI software in 203 (68.6%) patients while STDR was detected in 112 (37.8%) and 146 (49.3%) patients, respectively. The AI software showed 95.8% (95% CI 92.9-98.7) sensitivity and 80.2% (95% CI 72.6-87.8) specificity for detecting any DR and 99.1% (95% CI 95.1-99.9) sensitivity and 80.4% (95% CI 73.9-85.9) specificity in detecting STDR with a kappa agreement of k = 0.78 (p < 0.001) and k = 0.75 (p < 0.001), respectively. Automated AI analysis of FOP smartphone retinal imaging has very high sensitivity for detecting DR and STDR and thus can be an initial tool for mass retinal screening in people with diabetes.

EpHLA software: a timesaving and accurate tool for improving identification of acceptable mismatches for clinical purposes.

PubMed

Filho, Herton Luiz Alves Sales; da Mata Sousa, Luiz Claudio Demes; von Glehn, Cristina de Queiroz Carrascosa; da Silva, Adalberto Socorro; dos Santos Neto, Pedro de Alcântara; do Nascimento, Ferraz; de Castro, Adail Fonseca; do Nascimento, Liliane Machado; Kneib, Carolina; Bianchi Cazarote, Helena; Mayumi Kitamura, Daniele; Torres, Juliane Roberta Dias; da Cruz Lopes, Laiane; Barros, Aryela Loureiro; da Silva Edlin, Evelin Nildiane; de Moura, Fernanda Sá Leal; Watanabe, Janine Midori Figueiredo; do Monte, Semiramis Jamil Hadad

2012-06-01

The HLAMatchmaker algorithm, which allows the identification of “safe” acceptable mismatches (AMMs) for recipients of solid organ and cell allografts, is rarely used in part due to the difficulty in using it in the current Excel format. The automation of this algorithm may universalize its use to benefit the allocation of allografts. Recently, we have developed a new software called EpHLA, which is the first computer program automating the use of the HLAMatchmaker algorithm. Herein, we present the experimental validation of the EpHLA program by showing the time efficiency and the quality of operation. The same results, obtained by a single antigen bead assay with sera from 10 sensitized patients waiting for kidney transplants, were analyzed either by conventional HLAMatchmaker or by automated EpHLA method. Users testing these two methods were asked to record: (i) time required for completion of the analysis (in minutes); (ii) number of eplets obtained for class I and class II HLA molecules; (iii) categorization of eplets as reactive or non-reactive based on the MFI cutoff value; and (iv) determination of AMMs based on eplets' reactivities. We showed that although both methods had similar accuracy, the automated EpHLA method was over 8 times faster in comparison to the conventional HLAMatchmaker method. In particular the EpHLA software was faster and more reliable but equally accurate as the conventional method to define AMMs for allografts. The EpHLA software is an accurate and quick method for the identification of AMMs and thus it may be a very useful tool in the decision-making process of organ allocation for highly sensitized patients as well as in many other applications.

AutoDrug: fully automated macromolecular crystallography workflows for fragment-based drug discovery

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tsai, Yingssu; Stanford University, 333 Campus Drive, Mudd Building, Stanford, CA 94305-5080; McPhillips, Scott E.

New software has been developed for automating the experimental and data-processing stages of fragment-based drug discovery at a macromolecular crystallography beamline. A new workflow-automation framework orchestrates beamline-control and data-analysis software while organizing results from multiple samples. AutoDrug is software based upon the scientific workflow paradigm that integrates the Stanford Synchrotron Radiation Lightsource macromolecular crystallography beamlines and third-party processing software to automate the crystallography steps of the fragment-based drug-discovery process. AutoDrug screens a cassette of fragment-soaked crystals, selects crystals for data collection based on screening results and user-specified criteria and determines optimal data-collection strategies. It then collects and processes diffraction data,more » performs molecular replacement using provided models and detects electron density that is likely to arise from bound fragments. All processes are fully automated, i.e. are performed without user interaction or supervision. Samples can be screened in groups corresponding to particular proteins, crystal forms and/or soaking conditions. A single AutoDrug run is only limited by the capacity of the sample-storage dewar at the beamline: currently 288 samples. AutoDrug was developed in conjunction with RestFlow, a new scientific workflow-automation framework. RestFlow simplifies the design of AutoDrug by managing the flow of data and the organization of results and by orchestrating the execution of computational pipeline steps. It also simplifies the execution and interaction of third-party programs and the beamline-control system. Modeling AutoDrug as a scientific workflow enables multiple variants that meet the requirements of different user groups to be developed and supported. A workflow tailored to mimic the crystallography stages comprising the drug-discovery pipeline of CoCrystal Discovery Inc. has been deployed and successfully demonstrated. This workflow was run once on the same 96 samples that the group had examined manually and the workflow cycled successfully through all of the samples, collected data from the same samples that were selected manually and located the same peaks of unmodeled density in the resulting difference Fourier maps.« less

The development of a post-test diagnostic system for rocket engines

NASA Technical Reports Server (NTRS)

Zakrajsek, June F.

1991-01-01

An effort was undertaken by NASA to develop an automated post-test, post-flight diagnostic system for rocket engines. The automated system is designed to be generic and to automate the rocket engine data review process. A modular, distributed architecture with a generic software core was chosen to meet the design requirements. The diagnostic system is initially being applied to the Space Shuttle Main Engine data review process. The system modules currently under development are the session/message manager, and portions of the applications section, the component analysis section, and the intelligent knowledge server. An overview is presented of a rocket engine data review process, the design requirements and guidelines, the architecture and modules, and the projected benefits of the automated diagnostic system.

Geocoding uncertainty analysis for the automated processing of Sentinel-1 data using Sentinel-1 Toolbox software

NASA Astrophysics Data System (ADS)

Dostálová, Alena; Naeimi, Vahid; Wagner, Wolfgang; Elefante, Stefano; Cao, Senmao; Persson, Henrik

2016-10-01

One of the major advantages of the Sentinel-1 data is its capability to provide very high spatio-temporal coverage allowing the mapping of large areas as well as creation of dense time-series of the Sentinel-1 acquisitions. The SGRT software developed at TU Wien aims at automated processing of Sentinel-1 data for global and regional products. The first step of the processing consists of the Sentinel-1 data geocoding with the help of S1TBX software and their resampling to a common grid. These resampled images serve as an input for the product derivation. Thus, it is very important to select the most reliable processing settings and assess the geocoding uncertainty for both backscatter and projected local incidence angle images. Within this study, selection of Sentinel-1 acquisitions over 3 test areas in Europe were processed manually in the S1TBX software, testing multiple software versions, processing settings and digital elevation models (DEM) and the accuracy of the resulting geocoded images were assessed. Secondly, all available Sentinel-1 data over the areas were processed using selected settings and detailed quality check was performed. Overall, strong influence of the used DEM on the geocoding quality was confirmed with differences up to 80 meters in areas with higher terrain variations. In flat areas, the geocoding accuracy of backscatter images was overall good, with observed shifts between 0 and 30m. Larger systematic shifts were identified in case of projected local incidence angle images. These results encourage the automated processing of large volumes of Sentinel-1 data.

REDIR: Automated Static Detection of Obfuscated Anti-Debugging Techniques

DTIC Science & Technology

2014-03-27

analyzing code samples that resist other forms of analysis. 2.5.6 RODS and HASTI: Software Engineering Cognitive Support Software Engineering (SE) is another...and (c) this method is resistant to common obfuscation techniques. To achieve this goal, the Data/Frame sensemaking theory guides the process of...No Starch Press, 2012. [46] C.-W. Hsu, S. W. Shieh et al., “Divergence Detector: A Fine-Grained Approach to Detecting VM-Awareness Malware,” in

Transformation Systems at NASA Ames

NASA Technical Reports Server (NTRS)

Buntine, Wray; Fischer, Bernd; Havelund, Klaus; Lowry, Michael; Pressburger, TOm; Roach, Steve; Robinson, Peter; VanBaalen, Jeffrey

1999-01-01

In this paper, we describe the experiences of the Automated Software Engineering Group at the NASA Ames Research Center in the development and application of three different transformation systems. The systems span the entire technology range, from deductive synthesis, to logic-based transformation, to almost compiler-like source-to-source transformation. These systems also span a range of NASA applications, including solving solar system geometry problems, generating data analysis software, and analyzing multi-threaded Java code.

Power subsystem automation study

NASA Technical Reports Server (NTRS)

Tietz, J. C.; Sewy, D.; Pickering, C.; Sauers, R.

1984-01-01

The purpose of the phase 2 of the power subsystem automation study was to demonstrate the feasibility of using computer software to manage an aspect of the electrical power subsystem on a space station. The state of the art in expert systems software was investigated in this study. This effort resulted in the demonstration of prototype expert system software for managing one aspect of a simulated space station power subsystem.

Integrated optomechanical analysis and testing software development at MIT Lincoln Laboratory

NASA Astrophysics Data System (ADS)

Stoeckel, Gerhard P.; Doyle, Keith B.

2013-09-01

Advanced analytical software capabilities are being developed to advance the design of prototypical hardware in the Engineering Division at MIT Lincoln Laboratory. The current effort is focused on the integration of analysis tools tailored to the work flow, organizational structure, and current technology demands. These tools are being designed to provide superior insight into the interdisciplinary behavior of optical systems and enable rapid assessment and execution of design trades to optimize the design of optomechanical systems. The custom software architecture is designed to exploit and enhance the functionality of existing industry standard commercial software, provide a framework for centralizing internally developed tools, and deliver greater efficiency, productivity, and accuracy through standardization, automation, and integration. Specific efforts have included the development of a feature-rich software package for Structural-Thermal-Optical Performance (STOP) modeling, advanced Line Of Sight (LOS) jitter simulations, and improved integration of dynamic testing and structural modeling.

An overview of the Progenika ID CORE XT: an automated genotyping platform based on a fluidic microarray system.

PubMed

Goldman, Mindy; Núria, Núria; Castilho, Lilian M

2015-01-01

Automated testing platforms facilitate the introduction of red cell genotyping of patients and blood donors. Fluidic microarray systems, such as Luminex XMAP (Austin, TX), are used in many clinical applications, including HLA and HPA typing. The Progenika ID CORE XT (Progenika Biopharma-Grifols, Bizkaia, Spain) uses this platform to analyze 29 polymorphisms determining 37 antigens in 10 blood group systems. Once DNA has been extracted, processing time is approximately 4 hours. The system is highly automated and includes integrated analysis software that produces a file and a report with genotype and predicted phenotype results.

Spotlight-8 Image Analysis Software

NASA Technical Reports Server (NTRS)

Klimek, Robert; Wright, Ted

2006-01-01

Spotlight is a cross-platform GUI-based software package designed to perform image analysis on sequences of images generated by combustion and fluid physics experiments run in a microgravity environment. Spotlight can perform analysis on a single image in an interactive mode or perform analysis on a sequence of images in an automated fashion. Image processing operations can be employed to enhance the image before various statistics and measurement operations are performed. An arbitrarily large number of objects can be analyzed simultaneously with independent areas of interest. Spotlight saves results in a text file that can be imported into other programs for graphing or further analysis. Spotlight can be run on Microsoft Windows, Linux, and Apple OS X platforms.

Automated synthesis and composition of taskblocks for control of manufacturing systems.

PubMed

Holloway, L E; Guan, X; Sundaravadivelu, R; Ashley, J R

2000-01-01

Automated control synthesis methods for discrete-event systems promise to reduce the time required to develop, debug, and modify control software. Such methods must be able to translate high-level control goals into detailed sequences of actuation and sensing signals. In this paper, we present such a technique. It relies on analysis of a system model, defined as a set of interacting components, each represented as a form of condition system Petri net. Control logic modules, called taskblocks, are synthesized from these individual models. These then interact hierarchically and sequentially to drive the system through specified control goals. The resulting controller is automatically converted to executable control code. The paper concludes with a discussion of a set of software tools developed to demonstrate the techniques on a small manufacturing system.

Software and Algorithms for Biomedical Image Data Processing and Visualization

NASA Technical Reports Server (NTRS)

Talukder, Ashit; Lambert, James; Lam, Raymond

2004-01-01

A new software equipped with novel image processing algorithms and graphical-user-interface (GUI) tools has been designed for automated analysis and processing of large amounts of biomedical image data. The software, called PlaqTrak, has been specifically used for analysis of plaque on teeth of patients. New algorithms have been developed and implemented to segment teeth of interest from surrounding gum, and a real-time image-based morphing procedure is used to automatically overlay a grid onto each segmented tooth. Pattern recognition methods are used to classify plaque from surrounding gum and enamel, while ignoring glare effects due to the reflection of camera light and ambient light from enamel regions. The PlaqTrak system integrates these components into a single software suite with an easy-to-use GUI (see Figure 1) that allows users to do an end-to-end run of a patient s record, including tooth segmentation of all teeth, grid morphing of each segmented tooth, and plaque classification of each tooth image. The automated and accurate processing of the captured images to segment each tooth [see Figure 2(a)] and then detect plaque on a tooth-by-tooth basis is a critical component of the PlaqTrak system to do clinical trials and analysis with minimal human intervention. These features offer distinct advantages over other competing systems that analyze groups of teeth or synthetic teeth. PlaqTrak divides each segmented tooth into eight regions using an advanced graphics morphing procedure [see results on a chipped tooth in Figure 2(b)], and a pattern recognition classifier is then used to locate plaque [red regions in Figure 2(d)] and enamel regions. The morphing allows analysis within regions of teeth, thereby facilitating detailed statistical analysis such as the amount of plaque present on the biting surfaces on teeth. This software system is applicable to a host of biomedical applications, such as cell analysis and life detection, or robotic applications, such as product inspection or assembly of parts in space and industry.

Automated Quantitative Nuclear Cardiology Methods

PubMed Central

Motwani, Manish; Berman, Daniel S.; Germano, Guido; Slomka, Piotr J.

2016-01-01

Quantitative analysis of SPECT and PET has become a major part of nuclear cardiology practice. Current software tools can automatically segment the left ventricle, quantify function, establish myocardial perfusion maps and estimate global and local measures of stress/rest perfusion – all with minimal user input. State-of-the-art automated techniques have been shown to offer high diagnostic accuracy for detecting coronary artery disease, as well as predict prognostic outcomes. This chapter briefly reviews these techniques, highlights several challenges and discusses the latest developments. PMID:26590779

A taxonomy and discussion of software attack technologies

NASA Astrophysics Data System (ADS)

Banks, Sheila B.; Stytz, Martin R.

2005-03-01

Software is a complex thing. It is not an engineering artifact that springs forth from a design by simply following software coding rules; creativity and the human element are at the heart of the process. Software development is part science, part art, and part craft. Design, architecture, and coding are equally important activities and in each of these activities, errors may be introduced that lead to security vulnerabilities. Therefore, inevitably, errors enter into the code. Some of these errors are discovered during testing; however, some are not. The best way to find security errors, whether they are introduced as part of the architecture development effort or coding effort, is to automate the security testing process to the maximum extent possible and add this class of tools to the tools available, which aids in the compilation process, testing, test analysis, and software distribution. Recent technological advances, improvements in computer-generated forces (CGFs), and results in research in information assurance and software protection indicate that we can build a semi-intelligent software security testing tool. However, before we can undertake the security testing automation effort, we must understand the scope of the required testing, the security failures that need to be uncovered during testing, and the characteristics of the failures. Therefore, we undertook the research reported in the paper, which is the development of a taxonomy and a discussion of software attacks generated from the point of view of the security tester with the goal of using the taxonomy to guide the development of the knowledge base for the automated security testing tool. The representation for attacks and threat cases yielded by this research captures the strategies, tactics, and other considerations that come into play during the planning and execution of attacks upon application software. The paper is organized as follows. Section one contains an introduction to our research and a discussion of the motivation for our work. Section two contains a presents our taxonomy of software attacks and a discussion of the strategies employed and general weaknesses exploited for each attack. Section three contains a summary and suggestions for further research.

ConfocalCheck - A Software Tool for the Automated Monitoring of Confocal Microscope Performance

PubMed Central

Hng, Keng Imm; Dormann, Dirk

2013-01-01

Laser scanning confocal microscopy has become an invaluable tool in biomedical research but regular quality testing is vital to maintain the system’s performance for diagnostic and research purposes. Although many methods have been devised over the years to characterise specific aspects of a confocal microscope like measuring the optical point spread function or the field illumination, only very few analysis tools are available. Our aim was to develop a comprehensive quality assurance framework ranging from image acquisition to automated analysis and documentation. We created standardised test data to assess the performance of the lasers, the objective lenses and other key components required for optimum confocal operation. The ConfocalCheck software presented here analyses the data fully automatically. It creates numerous visual outputs indicating potential issues requiring further investigation. By storing results in a web browser compatible file format the software greatly simplifies record keeping allowing the operator to quickly compare old and new data and to spot developing trends. We demonstrate that the systematic monitoring of confocal performance is essential in a core facility environment and how the quantitative measurements obtained can be used for the detailed characterisation of system components as well as for comparisons across multiple instruments. PMID:24224017

Fuzzy Control/Space Station automation

NASA Technical Reports Server (NTRS)

Gersh, Mark

1990-01-01

Viewgraphs on fuzzy control/space station automation are presented. Topics covered include: Space Station Freedom (SSF); SSF evolution; factors pointing to automation & robotics (A&R); astronaut office inputs concerning A&R; flight system automation and ground operations applications; transition definition program; and advanced automation software tools.

Effectiveness of an automatic tracking software in underwater motion analysis.

PubMed

Magalhaes, Fabrício A; Sawacha, Zimi; Di Michele, Rocco; Cortesi, Matteo; Gatta, Giorgio; Fantozzi, Silvia

2013-01-01

Tracking of markers placed on anatomical landmarks is a common practice in sports science to perform the kinematic analysis that interests both athletes and coaches. Although different software programs have been developed to automatically track markers and/or features, none of them was specifically designed to analyze underwater motion. Hence, this study aimed to evaluate the effectiveness of a software developed for automatic tracking of underwater movements (DVP), based on the Kanade-Lucas-Tomasi feature tracker. Twenty-one video recordings of different aquatic exercises (n = 2940 markers' positions) were manually tracked to determine the markers' center coordinates. Then, the videos were automatically tracked using DVP and a commercially available software (COM). Since tracking techniques may produce false targets, an operator was instructed to stop the automatic procedure and to correct the position of the cursor when the distance between the calculated marker's coordinate and the reference one was higher than 4 pixels. The proportion of manual interventions required by the software was used as a measure of the degree of automation. Overall, manual interventions were 10.4% lower for DVP (7.4%) than for COM (17.8%). Moreover, when examining the different exercise modes separately, the percentage of manual interventions was 5.6% to 29.3% lower for DVP than for COM. Similar results were observed when analyzing the type of marker rather than the type of exercise, with 9.9% less manual interventions for DVP than for COM. In conclusion, based on these results, the developed automatic tracking software presented can be used as a valid and useful tool for underwater motion analysis. Key PointsThe availability of effective software for automatic tracking would represent a significant advance for the practical use of kinematic analysis in swimming and other aquatic sports.An important feature of automatic tracking software is to require limited human interventions and supervision, thus allowing short processing time.When tracking underwater movements, the degree of automation of the tracking procedure is influenced by the capability of the algorithm to overcome difficulties linked to the small target size, the low image quality and the presence of background clutters.The newly developed feature-tracking algorithm has shown a good automatic tracking effectiveness in underwater motion analysis with significantly smaller percentage of required manual interventions when compared to a commercial software.

Automated Performance Characterization of DSN System Frequency Stability Using Spacecraft Tracking Data

NASA Technical Reports Server (NTRS)

Pham, Timothy T.; Machuzak, Richard J.; Bedrossian, Alina; Kelly, Richard M.; Liao, Jason C.

2012-01-01

This software provides an automated capability to measure and qualify the frequency stability performance of the Deep Space Network (DSN) ground system, using daily spacecraft tracking data. The results help to verify if the DSN performance is meeting its specification, therefore ensuring commitments to flight missions; in particular, the radio science investigations. The rich set of data also helps the DSN Operations and Maintenance team to identify the trends and patterns, allowing them to identify the antennas of lower performance and implement corrective action in a timely manner. Unlike the traditional approach where the performance can only be obtained from special calibration sessions that are both time-consuming and require manual setup, the new method taps into the daily spacecraft tracking data. This new approach significantly increases the amount of data available for analysis, roughly by two orders of magnitude, making it possible to conduct trend analysis with good confidence. The software is built with automation in mind for end-to-end processing. From the inputs gathering to computation analysis and later data visualization of the results, all steps are done automatically, making the data production at near zero cost. This allows the limited engineering resource to focus on high-level assessment and to follow up with the exceptions/deviations. To make it possible to process the continual stream of daily incoming data without much effort, and to understand the results quickly, the processing needs to be automated and the data summarized at a high level. Special attention needs to be given to data gathering, input validation, handling anomalous conditions, computation, and presenting the results in a visual form that makes it easy to spot items of exception/ deviation so that further analysis can be directed and corrective actions followed.

Automated Performance Characterization of DSN System Frequency Stability Using Spacecraft Tracking Data

NASA Technical Reports Server (NTRS)

Pham, Timothy T.; Machuzak, Richard J.; Bedrossian, Alina; Kelly, Richard M.; Liao, Jason C.

2012-01-01

This software provides an automated capability to measure and qualify the frequency stability performance of the Deep Space Network (DSN) ground system, using daily spacecraft tracking data. The results help to verify if the DSN performance is meeting its specification, therefore ensuring commitments to flight missions; in particular, the radio science investigations. The rich set of data also helps the DSN Operations and Maintenance team to identify the trends and patterns, allowing them to identify the antennas of lower performance and implement corrective action in a timely manner. Unlike the traditional approach where the performance can only be obtained from special calibration sessions that are both time-consuming and require manual setup, the new method taps into the daily spacecraft tracking data. This new approach significantly increases the amount of data available for analysis, roughly by two orders of magnitude, making it possible to conduct trend analysis with good confidence. The software is built with automation in mind for end-to-end processing. From the inputs gathering to computation analysis and later data visualization of the results, all steps are done automatically, making the data production at near zero cost. This allows the limited engineering resource to focus on high-level assessment and to follow up with the exceptions/deviations. To make it possible to process the continual stream of daily incoming data without much effort, and to understand the results quickly, the processing needs to be automated and the data summarized at a high level. Special attention needs to be given to data gathering, input validation, handling anomalous conditions, computation, and presenting the results in a visual form that makes it easy to spot items of exception/deviation so that further analysis can be directed and corrective actions followed.

MAGE (M-file/Mif Automatic GEnerator): A graphical interface tool for automatic generation of Object Oriented Micromagnetic Framework configuration files and Matlab scripts for results analysis

NASA Astrophysics Data System (ADS)

Chęciński, Jakub; Frankowski, Marek

2016-10-01

We present a tool for fully-automated generation of both simulations configuration files (Mif) and Matlab scripts for automated data analysis, dedicated for Object Oriented Micromagnetic Framework (OOMMF). We introduce extended graphical user interface (GUI) that allows for fast, error-proof and easy creation of Mifs, without any programming skills usually required for manual Mif writing necessary. With MAGE we provide OOMMF extensions for complementing it by mangetoresistance and spin-transfer-torque calculations, as well as local magnetization data selection for output. Our software allows for creation of advanced simulations conditions like simultaneous parameters sweeps and synchronic excitation application. Furthermore, since output of such simulation could be long and complicated we provide another GUI allowing for automated creation of Matlab scripts suitable for analysis of such data with Fourier and wavelet transforms as well as user-defined operations.

Generating a Magellanic star cluster catalog with ASteCA

NASA Astrophysics Data System (ADS)

Perren, G. I.; Piatti, A. E.; Vázquez, R. A.

2016-08-01

An increasing number of software tools have been employed in the recent years for the automated or semi-automated processing of astronomical data. The main advantages of using these tools over a standard by-eye analysis include: speed (particularly for large databases), homogeneity, reproducibility, and precision. At the same time, they enable a statistically correct study of the uncertainties associated with the analysis, in contrast with manually set errors, or the still widespread practice of simply not assigning errors. We present a catalog comprising 210 star clusters located in the Large and Small Magellanic Clouds, observed with Washington photometry. Their fundamental parameters were estimated through an homogeneous, automatized and completely unassisted process, via the Automated Stellar Cluster Analysis package ( ASteCA). Our results are compared with two types of studies on these clusters: one where the photometry is the same, and another where the photometric system is different than that employed by ASteCA.

Automated three-dimensional quantification of myocardial perfusion and brain SPECT.

PubMed

Slomka, P J; Radau, P; Hurwitz, G A; Dey, D

2001-01-01

To allow automated and objective reading of nuclear medicine tomography, we have developed a set of tools for clinical analysis of myocardial perfusion tomography (PERFIT) and Brain SPECT/PET (BRASS). We exploit algorithms for image registration and use three-dimensional (3D) "normal models" for individual patient comparisons to composite datasets on a "voxel-by-voxel basis" in order to automatically determine the statistically significant abnormalities. A multistage, 3D iterative inter-subject registration of patient images to normal templates is applied, including automated masking of the external activity before final fit. In separate projects, the software has been applied to the analysis of myocardial perfusion SPECT, as well as brain SPECT and PET data. Automatic reading was consistent with visual analysis; it can be applied to the whole spectrum of clinical images, and aid physicians in the daily interpretation of tomographic nuclear medicine images.

Automated digital image analysis of islet cell mass using Nikon's inverted eclipse Ti microscope and software to improve engraftment may help to advance the therapeutic efficacy and accessibility of islet transplantation across centers.

PubMed

Gmyr, Valery; Bonner, Caroline; Lukowiak, Bruno; Pawlowski, Valerie; Dellaleau, Nathalie; Belaich, Sandrine; Aluka, Isanga; Moermann, Ericka; Thevenet, Julien; Ezzouaoui, Rimed; Queniat, Gurvan; Pattou, Francois; Kerr-Conte, Julie

2015-01-01

Reliable assessment of islet viability, mass, and purity must be met prior to transplanting an islet preparation into patients with type 1 diabetes. The standard method for quantifying human islet preparations is by direct microscopic analysis of dithizone-stained islet samples, but this technique may be susceptible to inter-/intraobserver variability, which may induce false positive/negative islet counts. Here we describe a simple, reliable, automated digital image analysis (ADIA) technique for accurately quantifying islets into total islet number, islet equivalent number (IEQ), and islet purity before islet transplantation. Islets were isolated and purified from n = 42 human pancreata according to the automated method of Ricordi et al. For each preparation, three islet samples were stained with dithizone and expressed as IEQ number. Islets were analyzed manually by microscopy or automatically quantified using Nikon's inverted Eclipse Ti microscope with built-in NIS-Elements Advanced Research (AR) software. The AIDA method significantly enhanced the number of islet preparations eligible for engraftment compared to the standard manual method (p < 0.001). Comparisons of individual methods showed good correlations between mean values of IEQ number (r(2) = 0.91) and total islet number (r(2) = 0.88) and thus increased to r(2) = 0.93 when islet surface area was estimated comparatively with IEQ number. The ADIA method showed very high intraobserver reproducibility compared to the standard manual method (p < 0.001). However, islet purity was routinely estimated as significantly higher with the manual method versus the ADIA method (p < 0.001). The ADIA method also detected small islets between 10 and 50 µm in size. Automated digital image analysis utilizing the Nikon Instruments software is an unbiased, simple, and reliable teaching tool to comprehensively assess the individual size of each islet cell preparation prior to transplantation. Implementation of this technology to improve engraftment may help to advance the therapeutic efficacy and accessibility of islet transplantation across centers.

MO-PIS-Exhibit Hall-01: Tools for TG-142 Linac Imaging QA I

DOE Office of Scientific and Technical Information (OSTI.GOV)

Clements, M; Wiesmeyer, M

2014-06-15

Partners in Solutions is an exciting new program in which AAPM partners with our vendors to present practical “hands-on” information about the equipment and software systems that we use in our clinics. The therapy topic this year is solutions for TG-142 recommendations for linear accelerator imaging QA. Note that the sessions are being held in a special purpose room built on the Exhibit Hall Floor, to encourage further interaction with the vendors. Automated Imaging QA for TG-142 with RIT Presentation Time: 2:45 – 3:15 PM This presentation will discuss software tools for automated imaging QA and phantom analysis for TG-142.more » All modalities used in radiation oncology will be discussed, including CBCT, planar kV imaging, planar MV imaging, and imaging and treatment coordinate coincidence. Vendor supplied phantoms as well as a variety of third-party phantoms will be shown, along with appropriate analyses, proper phantom setup procedures and scanning settings, and a discussion of image quality metrics. Tools for process automation will be discussed which include: RIT Cognition (machine learning for phantom image identification), RIT Cerberus (automated file system monitoring and searching), and RunQueueC (batch processing of multiple images). In addition to phantom analysis, tools for statistical tracking, trending, and reporting will be discussed. This discussion will include an introduction to statistical process control, a valuable tool in analyzing data and determining appropriate tolerances. An Introduction to TG-142 Imaging QA Using Standard Imaging Products Presentation Time: 3:15 – 3:45 PM Medical Physicists want to understand the logic behind TG-142 Imaging QA. What is often missing is a firm understanding of the connections between the EPID and OBI phantom imaging, the software “algorithms” that calculate the QA metrics, the establishment of baselines, and the analysis and interpretation of the results. The goal of our brief presentation will be to establish and solidify these connections. Our talk will be motivated by the Standard Imaging, Inc. phantom and software solutions. We will present and explain each of the image quality metrics in TG-142 in terms of the theory, mathematics, and algorithms used to implement them in the Standard Imaging PIPSpro software. In the process, we will identify the regions of phantom images that are analyzed by each algorithm. We then will discuss the process of the creation of baselines and typical ranges of acceptable values for each imaging quality metric.« less

Space station advanced automation

NASA Technical Reports Server (NTRS)

Woods, Donald

1990-01-01

In the development of a safe, productive and maintainable space station, Automation and Robotics (A and R) has been identified as an enabling technology which will allow efficient operation at a reasonable cost. The Space Station Freedom's (SSF) systems are very complex, and interdependent. The usage of Advanced Automation (AA) will help restructure, and integrate system status so that station and ground personnel can operate more efficiently. To use AA technology for the augmentation of system management functions requires a development model which consists of well defined phases of: evaluation, development, integration, and maintenance. The evaluation phase will consider system management functions against traditional solutions, implementation techniques and requirements; the end result of this phase should be a well developed concept along with a feasibility analysis. In the development phase the AA system will be developed in accordance with a traditional Life Cycle Model (LCM) modified for Knowledge Based System (KBS) applications. A way by which both knowledge bases and reasoning techniques can be reused to control costs is explained. During the integration phase the KBS software must be integrated with conventional software, and verified and validated. The Verification and Validation (V and V) techniques applicable to these KBS are based on the ideas of consistency, minimal competency, and graph theory. The maintenance phase will be aided by having well designed and documented KBS software.

Cost considerations in automating the library.

PubMed Central

Bolef, D

1987-01-01

The purchase price of a computer and its software is but a part of the cost of any automated system. There are many additional costs, including one-time costs of terminals, printers, multiplexors, microcomputers, consultants, workstations and retrospective conversion, and ongoing costs of maintenance and maintenance contracts for the equipment and software, telecommunications, and supplies. This paper examines those costs in an effort to produce a more realistic picture of an automated system. PMID:3594021

Performance analysis of automated evaluation of Crithidia luciliae-based indirect immunofluorescence tests in a routine setting - strengths and weaknesses.

PubMed

Hormann, Wymke; Hahn, Melanie; Gerlach, Stefan; Hochstrate, Nicola; Affeldt, Kai; Giesen, Joyce; Fechner, Kai; Damoiseaux, Jan G M C

2017-11-27

Antibodies directed against dsDNA are a highly specific diagnostic marker for the presence of systemic lupus erythematosus and of particular importance in its diagnosis. To assess anti-dsDNA antibodies, the Crithidia luciliae-based indirect immunofluorescence test (CLIFT) is one of the assays considered to be the best choice. To overcome the drawback of subjective result interpretation that inheres indirect immunofluorescence assays in general, automated systems have been introduced into the market during the last years. Among these systems is the EUROPattern Suite, an advanced automated fluorescence microscope equipped with different software packages, capable of automated pattern interpretation and result suggestion for ANA, ANCA and CLIFT analysis. We analyzed the performance of the EUROPattern Suite with its automated fluorescence interpretation for CLIFT in a routine setting, reflecting the everyday life of a diagnostic laboratory. Three hundred and twelve consecutive samples were collected, sent to the Central Diagnostic Laboratory of the Maastricht University Medical Centre with a request for anti-dsDNA analysis over a period of 7 months. Agreement between EUROPattern assay analysis and the visual read was 93.3%. Sensitivity and specificity were 94.1% and 93.2%, respectively. The EUROPattern Suite performed reliably and greatly supported result interpretation. Automated image acquisition is readily performed and automated image classification gives a reliable recommendation for assay evaluation to the operator. The EUROPattern Suite optimizes workflow and contributes to standardization between different operators or laboratories.

VoroTop: Voronoi cell topology visualization and analysis toolkit

NASA Astrophysics Data System (ADS)

Lazar, Emanuel A.

2018-01-01

This paper introduces a new open-source software program called VoroTop, which uses Voronoi topology to analyze local structure in atomic systems. Strengths of this approach include its abilities to analyze high-temperature systems and to characterize complex structure such as grain boundaries. This approach enables the automated analysis of systems and mechanisms previously not possible.

Yaxx: Yet another X-ray extractor

NASA Astrophysics Data System (ADS)

Aldcroft, Tom

2013-06-01

Yaxx is a Perl script that facilitates batch data processing using Perl open source software and commonly available software such as CIAO/Sherpa, S-lang, SAS, and FTOOLS. For Chandra and XMM analysis it includes automated spectral extraction, fitting, and report generation. Yaxx can be run without climbing an extensive learning curve; even so, yaxx is highly configurable and can be customized to support complex analysis. yaxx uses template files and takes full advantage of the unique Sherpa / S-lang environment to make much of the processing user configurable. Although originally developed with an emphasis on X-ray data analysis, yaxx evolved to be a general-purpose pipeline scripting package.

Hardware and software for automating the process of studying high-speed gas flows in wind tunnels of short-term action

NASA Astrophysics Data System (ADS)

Yakovlev, V. V.; Shakirov, S. R.; Gilyov, V. M.; Shpak, S. I.

2017-10-01

In this paper, we propose a variant of constructing automation systems for aerodynamic experiments on the basis of modern hardware-software means of domestic development. The structure of the universal control and data collection system for performing experiments in wind tunnels of continuous, periodic or short-term action is proposed. The proposed hardware and software development tools for ICT SB RAS and ITAM SB RAS, as well as subsystems based on them, can be widely applied to any scientific and experimental installations, as well as to the automation of technological processes in production.

Performance of automated and manual coding systems for occupational data: a case study of historical records.

PubMed

Patel, Mehul D; Rose, Kathryn M; Owens, Cindy R; Bang, Heejung; Kaufman, Jay S

2012-03-01

Occupational data are a common source of workplace exposure and socioeconomic information in epidemiologic research. We compared the performance of two occupation coding methods, an automated software and a manual coder, using occupation and industry titles from U.S. historical records. We collected parental occupational data from 1920-40s birth certificates, Census records, and city directories on 3,135 deceased individuals in the Atherosclerosis Risk in Communities (ARIC) study. Unique occupation-industry narratives were assigned codes by a manual coder and the Standardized Occupation and Industry Coding software program. We calculated agreement between coding methods of classification into major Census occupational groups. Automated coding software assigned codes to 71% of occupations and 76% of industries. Of this subset coded by software, 73% of occupation codes and 69% of industry codes matched between automated and manual coding. For major occupational groups, agreement improved to 89% (kappa = 0.86). Automated occupational coding is a cost-efficient alternative to manual coding. However, some manual coding is required to code incomplete information. We found substantial variability between coders in the assignment of occupations although not as large for major groups.

CoLiTec software - detection of the near-zero apparent motion

NASA Astrophysics Data System (ADS)

Khlamov, Sergii V.; Savanevych, Vadym E.; Briukhovetskyi, Olexandr B.; Pohorelov, Artem V.

2017-06-01

In this article we described CoLiTec software for full automated frames processing. CoLiTec software allows processing the Big Data of observation results as well as processing of data that is continuously formed during observation. The scope of solving tasks includes frames brightness equalization, moving objects detection, astrometry, photometry, etc. Along with the high efficiency of Big Data processing CoLiTec software also ensures high accuracy of data measurements. A comparative analysis of the functional characteristics and positional accuracy was performed between CoLiTec and Astrometrica software. The benefits of CoLiTec used with wide field and low quality frames were observed. The efficiency of the CoLiTec software was proved by about 700.000 observations and over 1.500 preliminary discoveries.

Space plasma research

NASA Technical Reports Server (NTRS)

Comfort, R. H.; Horwitz, J. L.

1986-01-01

Temperature and density analysis in the Automated Analysis Program (for the global empirical model) were modified to use flow velocities produced by the flow velocity analysis. Revisions were started to construct an interactive version of the technique for temperature and density analysis used in the automated analysis program. A sutdy of ion and electron heating at high altitudes in the outer plasmasphere was initiated. Also the analysis of the electron gun experiments on SCATHA were extended to include eclipse operations in order to test a hypothesis that there are interactions between the 50 to 100 eV beam and spacecraft generated photoelectrons. The MASSCOMP software to be used in taking and displaying data in the two-ion plasma experiment was tested and is now working satisfactorily. Papers published during the report period are listed.

IntraFace

PubMed Central

De la Torre, Fernando; Chu, Wen-Sheng; Xiong, Xuehan; Vicente, Francisco; Ding, Xiaoyu; Cohn, Jeffrey

2016-01-01

Within the last 20 years, there has been an increasing interest in the computer vision community in automated facial image analysis algorithms. This has been driven by applications in animation, market research, autonomous-driving, surveillance, and facial editing among others. To date, there exist several commercial packages for specific facial image analysis tasks such as facial expression recognition, facial attribute analysis or face tracking. However, free and easy-to-use software that incorporates all these functionalities is unavailable. This paper presents IntraFace (IF), a publicly-available software package for automated facial feature tracking, head pose estimation, facial attribute recognition, and facial expression analysis from video. In addition, IFincludes a newly develop technique for unsupervised synchrony detection to discover correlated facial behavior between two or more persons, a relatively unexplored problem in facial image analysis. In tests, IF achieved state-of-the-art results for emotion expression and action unit detection in three databases, FERA, CK+ and RU-FACS; measured audience reaction to a talk given by one of the authors; and discovered synchrony for smiling in videos of parent-infant interaction. IF is free of charge for academic use at http://www.humansensing.cs.cmu.edu/intraface/. PMID:27346987

Feasibility of rapid and automated importation of 3D echocardiographic left ventricular (LV) geometry into a finite element (FEM) analysis model

PubMed Central

Verhey, Janko F; Nathan, Nadia S

2004-01-01

Background Finite element method (FEM) analysis for intraoperative modeling of the left ventricle (LV) is presently not possible. Since 3D structural data of the LV is now obtainable using standard transesophageal echocardiography (TEE) devices intraoperatively, the present study describes a method to transfer this data into a commercially available FEM analysis system: ABAQUS©. Methods In this prospective study TomTec LV Analysis TEE© Software was used for semi-automatic endocardial border detection, reconstruction, and volume-rendering of the clinical 3D echocardiographic data. A newly developed software program MVCP FemCoGen©, written in Delphi, reformats the TomTec file structures in five patients for use in ABAQUS and allows visualization of regional deformation of the LV. Results This study demonstrates that a fully automated importation of 3D TEE data into FEM modeling is feasible and can be efficiently accomplished in the operating room. Conclusion For complete intraoperative 3D LV finite element analysis, three input elements are necessary: 1. time-gaited, reality-based structural information, 2. continuous LV pressure and 3. instantaneous tissue elastance. The first of these elements is now available using the methods presented herein. PMID:15473901

IntraFace.

PubMed

De la Torre, Fernando; Chu, Wen-Sheng; Xiong, Xuehan; Vicente, Francisco; Ding, Xiaoyu; Cohn, Jeffrey

2015-05-01

Within the last 20 years, there has been an increasing interest in the computer vision community in automated facial image analysis algorithms. This has been driven by applications in animation, market research, autonomous-driving, surveillance, and facial editing among others. To date, there exist several commercial packages for specific facial image analysis tasks such as facial expression recognition, facial attribute analysis or face tracking. However, free and easy-to-use software that incorporates all these functionalities is unavailable. This paper presents IntraFace (IF), a publicly-available software package for automated facial feature tracking, head pose estimation, facial attribute recognition, and facial expression analysis from video. In addition, IFincludes a newly develop technique for unsupervised synchrony detection to discover correlated facial behavior between two or more persons, a relatively unexplored problem in facial image analysis. In tests, IF achieved state-of-the-art results for emotion expression and action unit detection in three databases, FERA, CK+ and RU-FACS; measured audience reaction to a talk given by one of the authors; and discovered synchrony for smiling in videos of parent-infant interaction. IF is free of charge for academic use at http://www.humansensing.cs.cmu.edu/intraface/.

SIMA: Python software for analysis of dynamic fluorescence imaging data.

PubMed

Kaifosh, Patrick; Zaremba, Jeffrey D; Danielson, Nathan B; Losonczy, Attila

2014-01-01

Fluorescence imaging is a powerful method for monitoring dynamic signals in the nervous system. However, analysis of dynamic fluorescence imaging data remains burdensome, in part due to the shortage of available software tools. To address this need, we have developed SIMA, an open source Python package that facilitates common analysis tasks related to fluorescence imaging. Functionality of this package includes correction of motion artifacts occurring during in vivo imaging with laser-scanning microscopy, segmentation of imaged fields into regions of interest (ROIs), and extraction of signals from the segmented ROIs. We have also developed a graphical user interface (GUI) for manual editing of the automatically segmented ROIs and automated registration of ROIs across multiple imaging datasets. This software has been designed with flexibility in mind to allow for future extension with different analysis methods and potential integration with other packages. Software, documentation, and source code for the SIMA package and ROI Buddy GUI are freely available at http://www.losonczylab.org/sima/.

A report on SHARP (Spacecraft Health Automated Reasoning Prototype) and the Voyager Neptune encounter

NASA Technical Reports Server (NTRS)

Martin, R. G. (Editor); Atkinson, D. J.; James, M. L.; Lawson, D. L.; Porta, H. J.

1990-01-01

The development and application of the Spacecraft Health Automated Reasoning Prototype (SHARP) for the operations of the telecommunications systems and link analysis functions in Voyager mission operations are presented. An overview is provided of the design and functional description of the SHARP system as it was applied to Voyager. Some of the current problems and motivations for automation in real-time mission operations are discussed, as are the specific solutions that SHARP provides. The application of SHARP to Voyager telecommunications had the goal of being a proof-of-capability demonstration of artificial intelligence as applied to the problem of real-time monitoring functions in planetary mission operations. AS part of achieving this central goal, the SHARP application effort was also required to address the issue of the design of an appropriate software system architecture for a ground-based, highly automated spacecraft monitoring system for mission operations, including methods for: (1) embedding a knowledge-based expert system for fault detection, isolation, and recovery within this architecture; (2) acquiring, managing, and fusing the multiple sources of information used by operations personnel; and (3) providing information-rich displays to human operators who need to exercise the capabilities of the automated system. In this regard, SHARP has provided an excellent example of how advanced artificial intelligence techniques can be smoothly integrated with a variety of conventionally programmed software modules, as well as guidance and solutions for many questions about automation in mission operations.

Automatic Generation of Overlays and Offset Values Based on Visiting Vehicle Telemetry and RWS Visuals

NASA Technical Reports Server (NTRS)

Dunne, Matthew J.

2011-01-01

The development of computer software as a tool to generate visual displays has led to an overall expansion of automated computer generated images in the aerospace industry. These visual overlays are generated by combining raw data with pre-existing data on the object or objects being analyzed on the screen. The National Aeronautics and Space Administration (NASA) uses this computer software to generate on-screen overlays when a Visiting Vehicle (VV) is berthing with the International Space Station (ISS). In order for Mission Control Center personnel to be a contributing factor in the VV berthing process, computer software similar to that on the ISS must be readily available on the ground to be used for analysis. In addition, this software must perform engineering calculations and save data for further analysis.

Automated Analysis of ARM Binaries using the Low-Level Virtual Machine Compiler Framework

DTIC Science & Technology

2011-03-01

president to insist on keeping his smartphone [CNN09]. A self-proclaimed BlackBerry addict , President Obama fought hard to keep his mobile device after his... smartphone but renders a device non-functional on installation [FSe09][Hof07]. Complex interactions between hardware and software components both within... smartphone (which is a big assumption), the phone may still be vulnerable if the hardware or software does not correctly implement the design

Toward fully automated processing of dynamic susceptibility contrast perfusion MRI for acute ischemic cerebral stroke.

PubMed

Kim, Jinsuh; Leira, Enrique C; Callison, Richard C; Ludwig, Bryan; Moritani, Toshio; Magnotta, Vincent A; Madsen, Mark T

2010-05-01

We developed fully automated software for dynamic susceptibility contrast (DSC) MR perfusion-weighted imaging (PWI) to efficiently and reliably derive critical hemodynamic information for acute stroke treatment decisions. Brain MR PWI was performed in 80 consecutive patients with acute nonlacunar ischemic stroke within 24h after onset of symptom from January 2008 to August 2009. These studies were automatically processed to generate hemodynamic parameters that included cerebral blood flow and cerebral blood volume, and the mean transit time (MTT). To develop reliable software for PWI analysis, we used computationally robust algorithms including the piecewise continuous regression method to determine bolus arrival time (BAT), log-linear curve fitting, arrival time independent deconvolution method and sophisticated motion correction methods. An optimal arterial input function (AIF) search algorithm using a new artery-likelihood metric was also developed. Anatomical locations of the automatically determined AIF were reviewed and validated. The automatically computed BAT values were statistically compared with estimated BAT by a single observer. In addition, gamma-variate curve-fitting errors of AIF and inter-subject variability of AIFs were analyzed. Lastly, two observes independently assessed the quality and area of hypoperfusion mismatched with restricted diffusion area from motion corrected MTT maps and compared that with time-to-peak (TTP) maps using the standard approach. The AIF was identified within an arterial branch and enhanced areas of perfusion deficit were visualized in all evaluated cases. Total processing time was 10.9+/-2.5s (mean+/-s.d.) without motion correction and 267+/-80s (mean+/-s.d.) with motion correction on a standard personal computer. The MTT map produced with our software adequately estimated brain areas with perfusion deficit and was significantly less affected by random noise of the PWI when compared with the TTP map. Results of image quality assessment by two observers revealed that the MTT maps exhibited superior quality over the TTP maps (88% good rating of MTT as compared to 68% of TTP). Our software allowed fully automated deconvolution analysis of DSC PWI using proven efficient algorithms that can be applied to acute stroke treatment decisions. Our streamlined method also offers promise for further development of automated quantitative analysis of the ischemic penumbra. Copyright (c) 2009 Elsevier Ireland Ltd. All rights reserved.

Design and demonstration of automated data analysis algorithms for ultrasonic inspection of complex composite panels with bonds

NASA Astrophysics Data System (ADS)

Aldrin, John C.; Forsyth, David S.; Welter, John T.

2016-02-01

To address the data review burden and improve the reliability of the ultrasonic inspection of large composite structures, automated data analysis (ADA) algorithms have been developed to make calls on indications that satisfy the detection criteria and minimize false calls. The original design followed standard procedures for analyzing signals for time-of-flight indications and backwall amplitude dropout. However, certain complex panels with varying shape, ply drops and the presence of bonds can complicate this interpretation process. In this paper, enhancements to the automated data analysis algorithms are introduced to address these challenges. To estimate the thickness of the part and presence of bonds without prior information, an algorithm tracks potential backwall or bond-line signals, and evaluates a combination of spatial, amplitude, and time-of-flight metrics to identify bonded sections. Once part boundaries, thickness transitions and bonded regions are identified, feature extraction algorithms are applied to multiple sets of through-thickness and backwall C-scan images, for evaluation of both first layer through thickness and layers under bonds. ADA processing results are presented for a variety of complex test specimens with inserted materials and other test discontinuities. Lastly, enhancements to the ADA software interface are presented, which improve the software usability for final data review by the inspectors and support the certification process.

The Use of AMET and Automated Scripts for Model Evaluation

EPA Science Inventory

The Atmospheric Model Evaluation Tool (AMET) is a suite of software designed to facilitate the analysis and evaluation of meteorological and air quality models. AMET matches the model output for particular locations to the corresponding observed values from one or more networks ...

Toward an Efficient Icing CFD Process Using an Interactive Software Toolkit: Smagglce 2D

NASA Technical Reports Server (NTRS)

Vickerman, Mary B.; Choo, Yung K.; Schilling, Herbert W.; Baez, Marivell; Braun, Donald C.; Cotton, Barbara J.

2001-01-01

Two-dimensional CID analysis for iced airfoils can be a labor-intensive task. The software toolkit SmaggIce 2D is being developed to help streamline the CID process and provide the unique features needed for icing. When complete, it will include a combination of partially automated and fully interactive tools for all aspects of the tasks leading up to the flow analysis: geometry preparation, domain decomposition. block boundary demoralization. gridding, and linking with a flow solver. It also includes tools to perform ice shape characterization, an important aid in determining the relationship between ice characteristics and their effects on aerodynamic performance. Completed tools, work-in-progress, and planned features of the software toolkit are presented here.

Domain specific software architectures: Command and control

NASA Technical Reports Server (NTRS)

Braun, Christine; Hatch, William; Ruegsegger, Theodore; Balzer, Bob; Feather, Martin; Goldman, Neil; Wile, Dave

1992-01-01

GTE is the Command and Control contractor for the Domain Specific Software Architectures program. The objective of this program is to develop and demonstrate an architecture-driven, component-based capability for the automated generation of command and control (C2) applications. Such a capability will significantly reduce the cost of C2 applications development and will lead to improved system quality and reliability through the use of proven architectures and components. A major focus of GTE's approach is the automated generation of application components in particular subdomains. Our initial work in this area has concentrated in the message handling subdomain; we have defined and prototyped an approach that can automate one of the most software-intensive parts of C2 systems development. This paper provides an overview of the GTE team's DSSA approach and then presents our work on automated support for message processing.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miller, M.; Kempner, L. Jr.; Mueller, W. III

The concept of an Expert System is not new. It has been around since the days of the early computers when scientists had dreams of robot automation to do everything from washing windows to automobile design. This paper discusses an application of an expert system and addresses software development issues and various levels of expert system development form a structural engineering viewpoint. An expert system designed to aid the structural engineer in first order inelastic analysis of latticed steel transmission powers is presented. The utilization of expert systems with large numerical analysis programs is discussed along with the software developmentmore » of such a system.« less

Using Automated Theorem Provers to Certify Auto-Generated Aerospace Software

NASA Technical Reports Server (NTRS)

Denney, Ewen; Fischer, Bernd; Schumann, Johann

2004-01-01

We describe a system for the automated certification of safety properties of NASA software. The system uses Hoare-style program verification technology to generate proof obligations which are then processed by an automated first-order theorem prover (ATP). For full automation, however, the obligations must be aggressively preprocessed and simplified We describe the unique requirements this places on the ATP and demonstrate how the individual simplification stages, which are implemented by rewriting, influence the ability of the ATP to solve the proof tasks. Experiments on more than 25,000 tasks were carried out using Vampire, Spass, and e-setheo.

Human performance cognitive-behavioral modeling: a benefit for occupational safety.

PubMed

Gore, Brian F

2002-01-01

Human Performance Modeling (HPM) is a computer-aided job analysis software methodology used to generate predictions of complex human-automation integration and system flow patterns with the goal of improving operator and system safety. The use of HPM tools has recently been increasing due to reductions in computational cost, augmentations in the tools' fidelity, and usefulness in the generated output. An examination of an Air Man-machine Integration Design and Analysis System (Air MIDAS) model evaluating complex human-automation integration currently underway at NASA Ames Research Center will highlight the importance to occupational safety of considering both cognitive and physical aspects of performance when researching human error.

Human performance cognitive-behavioral modeling: a benefit for occupational safety

NASA Technical Reports Server (NTRS)

Gore, Brian F.

2002-01-01

Human Performance Modeling (HPM) is a computer-aided job analysis software methodology used to generate predictions of complex human-automation integration and system flow patterns with the goal of improving operator and system safety. The use of HPM tools has recently been increasing due to reductions in computational cost, augmentations in the tools' fidelity, and usefulness in the generated output. An examination of an Air Man-machine Integration Design and Analysis System (Air MIDAS) model evaluating complex human-automation integration currently underway at NASA Ames Research Center will highlight the importance to occupational safety of considering both cognitive and physical aspects of performance when researching human error.

Agile Acceptance Test–Driven Development of Clinical Decision Support Advisories: Feasibility of Using Open Source Software

PubMed Central

Baldwin, Krystal L; Kannan, Vaishnavi; Flahaven, Emily L; Parks, Cassandra J; Ott, Jason M; Willett, Duwayne L

2018-01-01

Background Moving to electronic health records (EHRs) confers substantial benefits but risks unintended consequences. Modern EHRs consist of complex software code with extensive local configurability options, which can introduce defects. Defects in clinical decision support (CDS) tools are surprisingly common. Feasible approaches to prevent and detect defects in EHR configuration, including CDS tools, are needed. In complex software systems, use of test–driven development and automated regression testing promotes reliability. Test–driven development encourages modular, testable design and expanding regression test coverage. Automated regression test suites improve software quality, providing a “safety net” for future software modifications. Each automated acceptance test serves multiple purposes, as requirements (prior to build), acceptance testing (on completion of build), regression testing (once live), and “living” design documentation. Rapid-cycle development or “agile” methods are being successfully applied to CDS development. The agile practice of automated test–driven development is not widely adopted, perhaps because most EHR software code is vendor-developed. However, key CDS advisory configuration design decisions and rules stored in the EHR may prove amenable to automated testing as “executable requirements.” Objective We aimed to establish feasibility of acceptance test–driven development of clinical decision support advisories in a commonly used EHR, using an open source automated acceptance testing framework (FitNesse). Methods Acceptance tests were initially constructed as spreadsheet tables to facilitate clinical review. Each table specified one aspect of the CDS advisory’s expected behavior. Table contents were then imported into a test suite in FitNesse, which queried the EHR database to automate testing. Tests and corresponding CDS configuration were migrated together from the development environment to production, with tests becoming part of the production regression test suite. Results We used test–driven development to construct a new CDS tool advising Emergency Department nurses to perform a swallowing assessment prior to administering oral medication to a patient with suspected stroke. Test tables specified desired behavior for (1) applicable clinical settings, (2) triggering action, (3) rule logic, (4) user interface, and (5) system actions in response to user input. Automated test suite results for the “executable requirements” are shown prior to building the CDS alert, during build, and after successful build. Conclusions Automated acceptance test–driven development and continuous regression testing of CDS configuration in a commercial EHR proves feasible with open source software. Automated test–driven development offers one potential contribution to achieving high-reliability EHR configuration. Vetting acceptance tests with clinicians elicits their input on crucial configuration details early during initial CDS design and iteratively during rapid-cycle optimization. PMID:29653922

Agile Acceptance Test-Driven Development of Clinical Decision Support Advisories: Feasibility of Using Open Source Software.

PubMed

Basit, Mujeeb A; Baldwin, Krystal L; Kannan, Vaishnavi; Flahaven, Emily L; Parks, Cassandra J; Ott, Jason M; Willett, Duwayne L

2018-04-13

Moving to electronic health records (EHRs) confers substantial benefits but risks unintended consequences. Modern EHRs consist of complex software code with extensive local configurability options, which can introduce defects. Defects in clinical decision support (CDS) tools are surprisingly common. Feasible approaches to prevent and detect defects in EHR configuration, including CDS tools, are needed. In complex software systems, use of test-driven development and automated regression testing promotes reliability. Test-driven development encourages modular, testable design and expanding regression test coverage. Automated regression test suites improve software quality, providing a "safety net" for future software modifications. Each automated acceptance test serves multiple purposes, as requirements (prior to build), acceptance testing (on completion of build), regression testing (once live), and "living" design documentation. Rapid-cycle development or "agile" methods are being successfully applied to CDS development. The agile practice of automated test-driven development is not widely adopted, perhaps because most EHR software code is vendor-developed. However, key CDS advisory configuration design decisions and rules stored in the EHR may prove amenable to automated testing as "executable requirements." We aimed to establish feasibility of acceptance test-driven development of clinical decision support advisories in a commonly used EHR, using an open source automated acceptance testing framework (FitNesse). Acceptance tests were initially constructed as spreadsheet tables to facilitate clinical review. Each table specified one aspect of the CDS advisory's expected behavior. Table contents were then imported into a test suite in FitNesse, which queried the EHR database to automate testing. Tests and corresponding CDS configuration were migrated together from the development environment to production, with tests becoming part of the production regression test suite. We used test-driven development to construct a new CDS tool advising Emergency Department nurses to perform a swallowing assessment prior to administering oral medication to a patient with suspected stroke. Test tables specified desired behavior for (1) applicable clinical settings, (2) triggering action, (3) rule logic, (4) user interface, and (5) system actions in response to user input. Automated test suite results for the "executable requirements" are shown prior to building the CDS alert, during build, and after successful build. Automated acceptance test-driven development and continuous regression testing of CDS configuration in a commercial EHR proves feasible with open source software. Automated test-driven development offers one potential contribution to achieving high-reliability EHR configuration. Vetting acceptance tests with clinicians elicits their input on crucial configuration details early during initial CDS design and iteratively during rapid-cycle optimization. ©Mujeeb A Basit, Krystal L Baldwin, Vaishnavi Kannan, Emily L Flahaven, Cassandra J Parks, Jason M Ott, Duwayne L Willett. Originally published in JMIR Medical Informatics (http://medinform.jmir.org), 13.04.2018.

Nonlinear analysis of the heartbeats in public patient ECGs using an automated PD2i algorithm for risk stratification of arrhythmic death

PubMed Central

Skinner, James E; Anchin, Jerry M; Weiss, Daniel N

2008-01-01

Heart rate variability (HRV) reflects both cardiac autonomic function and risk of arrhythmic death (AD). Reduced indices of HRV based on linear stochastic models are independent risk factors for AD in post-myocardial infarct cohorts. Indices based on nonlinear deterministic models have a significantly higher sensitivity and specificity for predicting AD in retrospective data. A need exists for nonlinear analytic software easily used by a medical technician. In the current study, an automated nonlinear algorithm, the time-dependent point correlation dimension (PD2i), was evaluated. The electrocardiogram (ECG) data were provided through an National Institutes of Health-sponsored internet archive (PhysioBank) and consisted of all 22 malignant arrhythmia ECG files (VF/VT) and 22 randomly selected arrhythmia files as the controls. The results were blindly calculated by automated software (Vicor 2.0, Vicor Technologies, Inc., Boca Raton, FL) and showed all analyzable VF/VT files had PD2i < 1.4 and all analyzable controls had PD2i > 1.4. Five VF/VT and six controls were excluded because surrogate testing showed the RR-intervals to contain noise, possibly resulting from the low digitization rate of the ECGs. The sensitivity was 100%, specificity 85%, relative risk > 100; p < 0.01, power > 90%. Thus, automated heartbeat analysis by the time-dependent nonlinear PD2i-algorithm can accurately stratify risk of AD in public data made available for competitive testing of algorithms. PMID:18728829

Software engineering and data management for automated payload experiment tool

NASA Technical Reports Server (NTRS)

Maddux, Gary A.; Provancha, Anna; Chattam, David

1994-01-01

The Microgravity Projects Office identified a need to develop a software package that will lead experiment developers through the development planning process, obtain necessary information, establish an electronic data exchange avenue, and allow easier manipulation/reformatting of the collected information. An MS-DOS compatible software package called the Automated Payload Experiment Tool (APET) has been developed and delivered. The objective of this task is to expand on the results of the APET work previously performed by UAH and provide versions of the software in a Macintosh and Windows compatible format.

Automated analysis of calcium spiking profiles with CaSA software: two case studies from root-microbe symbioses.

PubMed

Russo, Giulia; Spinella, Salvatore; Sciacca, Eva; Bonfante, Paola; Genre, Andrea

2013-12-26

Repeated oscillations in intracellular calcium (Ca2+) concentration, known as Ca2+ spiking signals, have been described in plants for a limited number of cellular responses to biotic or abiotic stimuli and most notably the common symbiotic signaling pathway (CSSP) which mediates the recognition by their plant hosts of two endosymbiotic microbes, arbuscular mycorrhizal (AM) fungi and nitrogen fixing rhizobia. The detailed analysis of the complexity and variability of the Ca2+ spiking patterns which have been revealed in recent studies requires both extensive datasets and sophisticated statistical tools. As a contribution, we have developed automated Ca2+ spiking analysis (CaSA) software that performs i) automated peak detection, ii) statistical analyses based on the detected peaks, iii) autocorrelation analysis of peak-to-peak intervals to highlight major traits in the spiking pattern.We have evaluated CaSA in two experimental studies. In the first, CaSA highlighted unpredicted differences in the spiking patterns induced in Medicago truncatula root epidermal cells by exudates of the AM fungus Gigaspora margarita as a function of the phosphate concentration in the growth medium of both host and fungus. In the second study we compared the spiking patterns triggered by either AM fungal or rhizobial symbiotic signals. CaSA revealed the existence of different patterns in signal periodicity, which are thought to contribute to the so-called Ca2+ signature. We therefore propose CaSA as a useful tool for characterizing oscillatory biological phenomena such as Ca2+ spiking.

Quantitative semi-automated analysis of morphogenesis with single-cell resolution in complex embryos.

PubMed

Giurumescu, Claudiu A; Kang, Sukryool; Planchon, Thomas A; Betzig, Eric; Bloomekatz, Joshua; Yelon, Deborah; Cosman, Pamela; Chisholm, Andrew D

2012-11-01

A quantitative understanding of tissue morphogenesis requires description of the movements of individual cells in space and over time. In transparent embryos, such as C. elegans, fluorescently labeled nuclei can be imaged in three-dimensional time-lapse (4D) movies and automatically tracked through early cleavage divisions up to ~350 nuclei. A similar analysis of later stages of C. elegans development has been challenging owing to the increased error rates of automated tracking of large numbers of densely packed nuclei. We present Nucleitracker4D, a freely available software solution for tracking nuclei in complex embryos that integrates automated tracking of nuclei in local searches with manual curation. Using these methods, we have been able to track >99% of all nuclei generated in the C. elegans embryo. Our analysis reveals that ventral enclosure of the epidermis is accompanied by complex coordinated migration of the neuronal substrate. We can efficiently track large numbers of migrating nuclei in 4D movies of zebrafish cardiac morphogenesis, suggesting that this approach is generally useful in situations in which the number, packing or dynamics of nuclei present challenges for automated tracking.

Software development environments: Status and trends

NASA Technical Reports Server (NTRS)

Duffel, Larry E.

1988-01-01

Currently software engineers are the essential integrating factors tying several components together. The components consist of process, methods, computers, tools, support environments, and software engineers. The engineers today empower the tools versus the tools empowering the engineers. Some of the issues in software engineering are quality, managing the software engineering process, and productivity. A strategy to accomplish this is to promote the evolution of software engineering from an ad hoc, labor intensive activity to a managed, technology supported discipline. This strategy may be implemented by putting the process under management control, adopting appropriate methods, inserting the technology that provides automated support for the process and methods, collecting automated tools into an integrated environment and educating the personnel.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Iverson, Aaron

Ra Power Management (RPM) has developed a cloud based software platform that manages the financial and operational functions of third party financed solar projects throughout their lifecycle. RPM’s software streamlines and automates the sales, financing, and management of a portfolio of solar assets. The software helps solar developers automate the most difficult aspects of asset management, leading to increased transparency, efficiency, and reduction in human error. More importantly, our platform will help developers save money by improving their operating margins

Experiments with Test Case Generation and Runtime Analysis

NASA Technical Reports Server (NTRS)

Artho, Cyrille; Drusinsky, Doron; Goldberg, Allen; Havelund, Klaus; Lowry, Mike; Pasareanu, Corina; Rosu, Grigore; Visser, Willem; Koga, Dennis (Technical Monitor)

2003-01-01

Software testing is typically an ad hoc process where human testers manually write many test inputs and expected test results, perhaps automating their execution in a regression suite. This process is cumbersome and costly. This paper reports preliminary results on an approach to further automate this process. The approach consists of combining automated test case generation based on systematically exploring the program's input domain, with runtime analysis, where execution traces are monitored and verified against temporal logic specifications, or analyzed using advanced algorithms for detecting concurrency errors such as data races and deadlocks. The approach suggests to generate specifications dynamically per input instance rather than statically once-and-for-all. The paper describes experiments with variants of this approach in the context of two examples, a planetary rover controller and a space craft fault protection system.

Image segmentation and dynamic lineage analysis in single-cell fluorescence microscopy.

PubMed

Wang, Quanli; Niemi, Jarad; Tan, Chee-Meng; You, Lingchong; West, Mike

2010-01-01

An increasingly common component of studies in synthetic and systems biology is analysis of dynamics of gene expression at the single-cell level, a context that is heavily dependent on the use of time-lapse movies. Extracting quantitative data on the single-cell temporal dynamics from such movies remains a major challenge. Here, we describe novel methods for automating key steps in the analysis of single-cell, fluorescent images-segmentation and lineage reconstruction-to recognize and track individual cells over time. The automated analysis iteratively combines a set of extended morphological methods for segmentation, and uses a neighborhood-based scoring method for frame-to-frame lineage linking. Our studies with bacteria, budding yeast and human cells, demonstrate the portability and usability of these methods, whether using phase, bright field or fluorescent images. These examples also demonstrate the utility of our integrated approach in facilitating analyses of engineered and natural cellular networks in diverse settings. The automated methods are implemented in freely available, open-source software.

Acoustic Emission Analysis Applet (AEAA) Software

NASA Technical Reports Server (NTRS)

Nichols, Charles T.; Roth, Don J.

2013-01-01

NASA Glenn Research and NASA White Sands Test Facility have developed software supporting an automated pressure vessel structural health monitoring (SHM) system based on acoustic emissions (AE). The software, referred to as the Acoustic Emission Analysis Applet (AEAA), provides analysts with a tool that can interrogate data collected on Digital Wave Corp. and Physical Acoustics Corp. software using a wide spectrum of powerful filters and charts. This software can be made to work with any data once the data format is known. The applet will compute basic AE statistics, and statistics as a function of time and pressure (see figure). AEAA provides value added beyond the analysis provided by the respective vendors' analysis software. The software can handle data sets of unlimited size. A wide variety of government and commercial applications could benefit from this technology, notably requalification and usage tests for compressed gas and hydrogen-fueled vehicles. Future enhancements will add features similar to a "check engine" light on a vehicle. Once installed, the system will ultimately be used to alert International Space Station crewmembers to critical structural instabilities, but will have little impact to missions otherwise. Diagnostic information could then be transmitted to experienced technicians on the ground in a timely manner to determine whether pressure vessels have been impacted, are structurally unsound, or can be safely used to complete the mission.

Development of a Software Tool to Automate ADCO Flight Controller Console Planning Tasks

NASA Technical Reports Server (NTRS)

Anderson, Mark G.

2011-01-01

This independent study project covers the development of the International Space Station (ISS) Attitude Determination and Control Officer (ADCO) Planning Exchange APEX Tool. The primary goal of the tool is to streamline existing manual and time-intensive planning tools into a more automated, user-friendly application that interfaces with existing products and allows the ADCO to produce accurate products and timelines more effectively. This paper will survey the current ISS attitude planning process and its associated requirements, goals, documentation and software tools and how a software tool could simplify and automate many of the planning actions which occur at the ADCO console. The project will be covered from inception through the initial prototype delivery in November 2011 and will include development of design requirements and software as well as design verification and testing.

Off-the-shelf mobile handset environments for deploying accelerometer based gait and activity analysis algorithms.

PubMed

Hynes, Martin; Wang, Han; Kilmartin, Liam

2009-01-01

Over the last decade, there has been substantial research interest in the application of accelerometry data for many forms of automated gait and activity analysis algorithms. This paper introduces a summary of new "of-the-shelf" mobile phone handset platforms containing embedded accelerometers which support the development of custom software to implement real time analysis of the accelerometer data. An overview of the main software programming environments which support the development of such software, including Java ME based JSR 256 API, C++ based Motion Sensor API and the Python based "aXYZ" module, is provided. Finally, a sample application is introduced and its performance evaluated in order to illustrate how a standard mobile phone can be used to detect gait activity using such a non-intrusive and easily accepted sensing platform.

Automated Antibody De Novo Sequencing and Its Utility in Biopharmaceutical Discovery

NASA Astrophysics Data System (ADS)

Sen, K. Ilker; Tang, Wilfred H.; Nayak, Shruti; Kil, Yong J.; Bern, Marshall; Ozoglu, Berk; Ueberheide, Beatrix; Davis, Darryl; Becker, Christopher

2017-05-01

Applications of antibody de novo sequencing in the biopharmaceutical industry range from the discovery of new antibody drug candidates to identifying reagents for research and determining the primary structure of innovator products for biosimilar development. When murine, phage display, or patient-derived monoclonal antibodies against a target of interest are available, but the cDNA or the original cell line is not, de novo protein sequencing is required to humanize and recombinantly express these antibodies, followed by in vitro and in vivo testing for functional validation. Availability of fully automated software tools for monoclonal antibody de novo sequencing enables efficient and routine analysis. Here, we present a novel method to automatically de novo sequence antibodies using mass spectrometry and the Supernovo software. The robustness of the algorithm is demonstrated through a series of stress tests.

High-resolution, continuous field-of-view (FOV), non-rotating imaging system

NASA Technical Reports Server (NTRS)

Huntsberger, Terrance L. (Inventor); Stirbl, Robert C. (Inventor); Aghazarian, Hrand (Inventor); Padgett, Curtis W. (Inventor)

2010-01-01

A high resolution CMOS imaging system especially suitable for use in a periscope head. The imaging system includes a sensor head for scene acquisition, and a control apparatus inclusive of distributed processors and software for device-control, data handling, and display. The sensor head encloses a combination of wide field-of-view CMOS imagers and narrow field-of-view CMOS imagers. Each bank of imagers is controlled by a dedicated processing module in order to handle information flow and image analysis of the outputs of the camera system. The imaging system also includes automated or manually controlled display system and software for providing an interactive graphical user interface (GUI) that displays a full 360-degree field of view and allows the user or automated ATR system to select regions for higher resolution inspection.

Analysis of sulfates on low molecular weight heparin using mass spectrometry: structural characterization of enoxaparin.

PubMed

Gupta, Rohitesh; Ponnusamy, Moorthy P

2018-05-31

Structural characterization of low molecular weight heparin (LMWH) is critical to meet biosimilarity standards. In this context, the review focuses on structural analysis of labile sulfates attached to the side-groups of LMWH using mass spectrometry. A comprehensive review of this topic will help readers to identify key strategies for tackling the problem related to sulfate loss. At the same time, various mass spectrometry techniques are presented to facilitate compositional analysis of LMWH, mainly enoxaparin. Areas covered: This review summarizes findings on mass spectrometry application for LMWH, including modulation of sulfates, using enzymology and sample preparation approaches. Furthermore, popular open-source software packages for automated spectral data interpretation are also discussed. Successful use of LC/MS can decipher structural composition for LMWH and help evaluate their sameness or biosimilarity with the innovator molecule. Overall, the literature has been searched using PubMed by typing various search queries such as 'enoxaparin', 'mass spectrometry', 'low molecular weight heparin', 'structural characterization', etc. Expert commentary: This section highlights clinically relevant areas that need improvement to achieve satisfactory commercialization of LMWHs. It also primarily emphasizes the advancements in instrumentation related to mass spectrometry, and discusses building automated software for data interpretation and analysis.

Supervised Semi-Automated Data Analysis Software for Gas Chromatography / Differential Mobility Spectrometry (GC/DMS) Metabolomics Applications.

PubMed

Peirano, Daniel J; Pasamontes, Alberto; Davis, Cristina E

2016-09-01

Modern differential mobility spectrometers (DMS) produce complex and multi-dimensional data streams that allow for near-real-time or post-hoc chemical detection for a variety of applications. An active area of interest for this technology is metabolite monitoring for biological applications, and these data sets regularly have unique technical and data analysis end user requirements. While there are initial publications on how investigators have individually processed and analyzed their DMS metabolomic data, there are no user-ready commercial or open source software packages that are easily used for this purpose. We have created custom software uniquely suited to analyze gas chromatograph / differential mobility spectrometry (GC/DMS) data from biological sources. Here we explain the implementation of the software, describe the user features that are available, and provide an example of how this software functions using a previously-published data set. The software is compatible with many commercial or home-made DMS systems. Because the software is versatile, it can also potentially be used for other similarly structured data sets, such as GC/GC and other IMS modalities.

Data management in large-scale collaborative toxicity studies: how to file experimental data for automated statistical analysis.

PubMed

Stanzel, Sven; Weimer, Marc; Kopp-Schneider, Annette

2013-06-01

High-throughput screening approaches are carried out for the toxicity assessment of a large number of chemical compounds. In such large-scale in vitro toxicity studies several hundred or thousand concentration-response experiments are conducted. The automated evaluation of concentration-response data using statistical analysis scripts saves time and yields more consistent results in comparison to data analysis performed by the use of menu-driven statistical software. Automated statistical analysis requires that concentration-response data are available in a standardised data format across all compounds. To obtain consistent data formats, a standardised data management workflow must be established, including guidelines for data storage, data handling and data extraction. In this paper two procedures for data management within large-scale toxicological projects are proposed. Both procedures are based on Microsoft Excel files as the researcher's primary data format and use a computer programme to automate the handling of data files. The first procedure assumes that data collection has not yet started whereas the second procedure can be used when data files already exist. Successful implementation of the two approaches into the European project ACuteTox is illustrated. Copyright © 2012 Elsevier Ltd. All rights reserved.

StimDuino: an Arduino-based electrophysiological stimulus isolator.

PubMed

Sheinin, Anton; Lavi, Ayal; Michaelevski, Izhak

2015-03-30

Electrical stimulus isolator is a widely used device in electrophysiology. The timing of the stimulus application is usually automated and controlled by the external device or acquisition software; however, the intensity of the stimulus is adjusted manually. Inaccuracy, lack of reproducibility and no automation of the experimental protocol are disadvantages of the manual adjustment. To overcome these shortcomings, we developed StimDuino, an inexpensive Arduino-controlled stimulus isolator allowing highly accurate, reproducible automated setting of the stimulation current. The intensity of the stimulation current delivered by StimDuino is controlled by Arduino, an open-source microcontroller development platform. The automatic stimulation patterns are software-controlled and the parameters are set from Matlab-coded simple, intuitive and user-friendly graphical user interface. The software also allows remote control of the device over the network. Electrical current measurements showed that StimDuino produces the requested current output with high accuracy. In both hippocampal slice and in vivo recordings, the fEPSP measurements obtained with StimDuino and the commercial stimulus isolators showed high correlation. Commercial stimulus isolators are manually managed, while StimDuino generates automatic stimulation patterns with increasing current intensity. The pattern is utilized for the input-output relationship analysis, necessary for assessment of excitability. In contrast to StimuDuino, not all commercial devices are capable for remote control of the parameters and stimulation process. StimDuino-generated automation of the input-output relationship assessment eliminates need for the current intensity manually adjusting, improves stimulation reproducibility, accuracy and allows on-site and remote control of the stimulation parameters. Copyright © 2015 Elsevier B.V. All rights reserved.

Automated video surveillance: teaching an old dog new tricks

NASA Astrophysics Data System (ADS)

McLeod, Alastair

1993-12-01

The automated video surveillance market is booming with new players, new systems, new hardware and software, and an extended range of applications. This paper reviews available technology, and describes the features required for a good automated surveillance system. Both hardware and software are discussed. An overview of typical applications is also given. A shift towards PC-based hybrid systems, use of parallel processing, neural networks, and exploitation of modern telecomms are introduced, highlighting the evolution modern video surveillance systems.

Automated image analysis of placental villi and syncytial knots in histological sections.

PubMed

Kidron, Debora; Vainer, Ifat; Fisher, Yael; Sharony, Reuven

2017-05-01

Delayed villous maturation and accelerated villous maturation diagnosed in histologic sections are morphologic manifestations of pathophysiological conditions. The inter-observer agreement among pathologists in assessing these conditions is moderate at best. We investigated whether automated image analysis of placental villi and syncytial knots could improve standardization in diagnosing these conditions. Placentas of antepartum fetal death at or near term were diagnosed as normal, delayed or accelerated villous maturation. Histologic sections of 5 cases per group were photographed at ×10 magnification. Automated image analysis of villi and syncytial knots was performed, using ImageJ public domain software. Analysis of hundreds of histologic images was carried out within minutes on a personal computer, using macro commands. Compared to normal placentas, villi from delayed maturation were larger and fewer, with fewer and smaller syncytial knots. Villi from accelerated maturation were smaller. The data were further analyzed according to horizontal placental zones and groups of villous size. Normal placentas can be discriminated from placentas of delayed or accelerated villous maturation using automated image analysis. Automated image analysis of villi and syncytial knots is not equivalent to interpretation by the human eye. Each method has advantages and disadvantages in assessing the 2-dimensional histologic sections representing the complex, 3-dimensional villous tree. Image analysis of placentas provides quantitative data that might help in standardizing and grading of placentas for diagnostic and research purposes. Copyright © 2017 Elsevier Ltd. All rights reserved.

Multidisciplinary Tool for Systems Analysis of Planetary Entry, Descent, and Landing

NASA Technical Reports Server (NTRS)

Samareh, Jamshid A.

2011-01-01

Systems analysis of a planetary entry (SAPE), descent, and landing (EDL) is a multidisciplinary activity in nature. SAPE improves the performance of the systems analysis team by automating and streamlining the process, and this improvement can reduce the errors that stem from manual data transfer among discipline experts. SAPE is a multidisciplinary tool for systems analysis of planetary EDL for Venus, Earth, Mars, Jupiter, Saturn, Uranus, Neptune, and Titan. It performs EDL systems analysis for any planet, operates cross-platform (i.e., Windows, Mac, and Linux operating systems), uses existing software components and open-source software to avoid software licensing issues, performs low-fidelity systems analysis in one hour on a computer that is comparable to an average laptop, and keeps discipline experts in the analysis loop. SAPE uses Python, a platform-independent, open-source language, for integration and for the user interface. Development has relied heavily on the object-oriented programming capabilities that are available in Python. Modules are provided to interface with commercial and government off-the-shelf software components (e.g., thermal protection systems and finite-element analysis). SAPE currently includes the following analysis modules: geometry, trajectory, aerodynamics, aerothermal, thermal protection system, and interface for structural sizing.

SEM AutoAnalysis: enhancing photomask and NIL defect disposition and review

NASA Astrophysics Data System (ADS)

Schulz, Kristian; Egodage, Kokila; Tabbone, Gilles; Ehrlich, Christian; Garetto, Anthony

2017-06-01

For defect disposition and repair verification regarding printability, AIMS™ is the state of the art measurement tool in industry. With its unique capability of capturing aerial images of photomasks it is the one method that comes closest to emulating the printing behaviour of a scanner. However for nanoimprint lithography (NIL) templates aerial images cannot be applied to evaluate the success of a repair process. Hence, for NIL defect dispositioning scanning, electron microscopy (SEM) imaging is the method of choice. In addition, it has been a standard imaging method for further root cause analysis of defects and defect review on optical photomasks which enables 2D or even 3D mask profiling at high resolutions. In recent years a trend observed in mask shops has been the automation of processes that traditionally were driven by operators. This of course has brought many advantages one of which is freeing cost intensive labour from conducting repetitive and tedious work. Furthermore, it reduces variability in processes due to different operator skill and experience levels which at the end contributes to eliminating the human factor. Taking these factors into consideration, one of the software based solutions available under the FAVOR® brand to support customer needs is the aerial image evaluation software, AIMS™ AutoAnalysis (AAA). It provides fully automated analysis of AIMS™ images and runs in parallel to measurements. This is enabled by its direct connection and communication with the AIMS™tools. As one of many positive outcomes, generating automated result reports is facilitated, standardizing the mask manufacturing workflow. Today, AAA has been successfully introduced into production at multiple customers and is supporting the workflow as described above. These trends indeed have triggered the demand for similar automation with respect to SEM measurements leading to the development of SEM AutoAnalysis (SAA). It aims towards a fully automated SEM image evaluation process utilizing a completely different algorithm due to the different nature of SEM images and aerial images. Both AAA and SAA are the building blocks towards an image evaluation suite in the mask shop industry.

Automated designation of tie-points for image-to-image coregistration.

Treesearch

R.E. Kennedy; W.B. Cohen

2003-01-01

Image-to-image registration requires identification of common points in both images (image tie-points: ITPs). Here we describe software implementing an automated, area-based technique for identifying ITPs. The ITP software was designed to follow two strategies: ( I ) capitalize on human knowledge and pattern recognition strengths, and (2) favour robustness in many...

Using Software Tools to Automate the Assessment of Student Programs.

ERIC Educational Resources Information Center

Jackson, David

1991-01-01

Argues that advent of computer-aided instruction (CAI) systems for teaching introductory computer programing makes it imperative that software be developed to automate assessment and grading of student programs. Examples of typical student programing problems are given, and application of the Unix tools Lex and Yacc to the automatic assessment of…

Default Parallels Plesk Panel Page

Science.gov Websites

services that small businesses want and need. Our software includes key building blocks of cloud service virtualized servers Service Provider Products Parallels® Automation Hosting, SaaS, and cloud computing , the leading hosting automation software. You see this page because there is no Web site at this

Library Automation Alternatives in 1996 and User Satisfaction Ratings of Library Users by Operating System.

ERIC Educational Resources Information Center

Cibbarelli, Pamela

1996-01-01

Examines library automation product introductions and conversions to new operating systems. Compares user satisfaction ratings of the following library software packages: DOS/Windows, UNIX, Macintosh, and DEC VAX/VMS. Software is rated according to documentation, service/support, training, product reliability, product capabilities, ease of use,…

Multi-modality 3D breast imaging with X-Ray tomosynthesis and automated ultrasound.

PubMed

Sinha, Sumedha P; Roubidoux, Marilyn A; Helvie, Mark A; Nees, Alexis V; Goodsitt, Mitchell M; LeCarpentier, Gerald L; Fowlkes, J Brian; Chalek, Carl L; Carson, Paul L

2007-01-01

This study evaluated the utility of 3D automated ultrasound in conjunction with 3D digital X-Ray tomosynthesis for breast cancer detection and assessment, to better localize and characterize lesions in the breast. Tomosynthesis image volumes and automated ultrasound image volumes were acquired in the same geometry and in the same view for 27 patients. 3 MQSA certified radiologists independently reviewed the image volumes, visually correlating the images from the two modalities with in-house software. More sophisticated software was used on a smaller set of 10 cases, which enabled the radiologist to draw a 3D box around the suspicious lesion in one image set and isolate an anatomically correlated, similarly boxed region in the other modality image set. In the primary study, correlation was found to be moderately useful to the readers. In the additional study, using improved software, the median usefulness rating increased and confidence in localizing and identifying the suspicious mass increased in more than half the cases. As automated scanning and reading software techniques advance, superior results are expected.

Somatostatin receptor immunohistochemistry in neuroendocrine tumors: comparison between manual and automated evaluation

PubMed Central

Daniel, Kaemmerer; Maria, Athelogou; Amelie, Lupp; Isabell, Lenhardt; Stefan, Schulz; Luisa, Peter; Merten, Hommann; Vikas, Prasad; Gerd, Binnig; Paul, Baum Richard

2014-01-01

Background: Manual evaluation of somatostatin receptor (SSTR) immunohistochemistry (IHC) is a time-consuming and cost-intensive procedure. Aim of the study was to compare manual evaluation of SSTR subtype IHC to an automated software-based analysis, and to in-vivo imaging by SSTR-based PET/CT. Methods: We examined 25 gastroenteropancreatic neuroendocrine tumor (GEP-NET) patients and correlated their in-vivo SSTR-PET/CT data (determined by the standardized uptake values SUVmax,-mean) with the corresponding ex-vivo IHC data of SSTR subtype (1, 2A, 4, 5) expression. Exactly the same lesions were imaged by PET/CT, resected and analyzed by IHC in each patient. After manual evaluation, the IHC slides were digitized and automatically evaluated for SSTR expression by Definiens XD software. A virtual IHC score “BB1” was created for comparing the manual and automated analysis of SSTR expression. Results: BB1 showed a significant correlation with the corresponding conventionally determined Her2/neu score of the SSTR-subtypes 2A (rs: 0.57), 4 (rs: 0.44) and 5 (rs: 0.43). BB1 of SSTR2A also significantly correlated with the SUVmax (rs: 0.41) and the SUVmean (rs: 0.50). Likewise, a significant correlation was seen between the conventionally evaluated SSTR2A status and the SUVmax (rs: 0.42) and SUVmean (rs: 0.62).Conclusion: Our data demonstrate that the evaluation of the SSTR status by automated analysis (BB1 score), using digitized histopathology slides (“virtual microscopy”), corresponds well with the SSTR2A, 4 and 5 expression as determined by conventional manual histopathology. The BB1 score also exhibited a significant association to the SSTR-PET/CT data in accordance with the high affinity profile of the SSTR analogues used for imaging. PMID:25197368

An evolutionary solution to anesthesia automated record keeping.

PubMed

Bicker, A A; Gage, J S; Poppers, P J

1998-08-01

In the course of five years the development of an automated anesthesia record keeper has evolved through nearly a dozen stages, each marked by new features and sophistication. Commodity PC hardware and software minimized development costs. Object oriented analysis, programming and design supported the process of change. In addition, we developed an evolutionary strategy that optimized motivation, risk management, and maximized return on investment. Besides providing record keeping services, the system supports educational and research activities and through a flexible plotting paradigm, supports each anesthesiologist's focus on physiological data during and after anesthesia.

Methodology for automating software systems. Task 1 of the foundations for automating software systems

NASA Technical Reports Server (NTRS)

Moseley, Warren

1989-01-01

The early stages of a research program designed to establish an experimental research platform for software engineering are described. Major emphasis is placed on Computer Assisted Software Engineering (CASE). The Poor Man's CASE Tool is based on the Apple Macintosh system, employing available software including Focal Point II, Hypercard, XRefText, and Macproject. These programs are functional in themselves, but through advanced linking are available for operation from within the tool being developed. The research platform is intended to merge software engineering technology with artificial intelligence (AI). In the first prototype of the PMCT, however, the sections of AI are not included. CASE tools assist the software engineer in planning goals, routes to those goals, and ways to measure progress. The method described allows software to be synthesized instead of being written or built.

Development of an automated film-reading system for ballistic ranges

NASA Technical Reports Server (NTRS)

Yates, Leslie A.

1992-01-01

Software for an automated film-reading system that uses personal computers and digitized shadowgraphs is described. The software identifies pixels associated with fiducial-line and model images, and least-squares procedures are used to calculate the positions and orientations of the images. Automated position and orientation readings for sphere and cone models are compared to those obtained using a manual film reader. When facility calibration errors are removed from these readings, the accuracy of the automated readings is better than the pixel resolution, and it is equal to, or better than, the manual readings. The effects of film-reading and facility-calibration errors on calculated aerodynamic coefficients is discussed.

Administrative automation in a scientific environment

NASA Technical Reports Server (NTRS)

Jarrett, J. R.

1984-01-01

Although the scientific personnel at GSFC were advanced in the development and use of hardware and software for scientific applications, resistance to the use of automation or purchase of terminals, software and services, specifically for administrative functions was widespread. The approach used to address problems and constraints and plans for administrative automation within the Space and Earth Sciences Directorate are delineated. Accomplishments thus far include reduction of paperwork and manual efforts; improved communications through telemail and committees; additional support staff; increased awareness at all levels on ergonomic concerns and the need for training; better equipment; improved ADP skills through experience; management commitment; and an overall strategy for automating.

First Annual Workshop on Space Operations Automation and Robotics (SOAR 87)

NASA Technical Reports Server (NTRS)

Griffin, Sandy (Editor)

1987-01-01

Several topics relative to automation and robotics technology are discussed. Automation of checkout, ground support, and logistics; automated software development; man-machine interfaces; neural networks; systems engineering and distributed/parallel processing architectures; and artificial intelligence/expert systems are among the topics covered.

SU-G-BRB-02: An Open-Source Software Analysis Library for Linear Accelerator Quality Assurance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kerns, J; Yaldo, D

Purpose: Routine linac quality assurance (QA) tests have become complex enough to require automation of most test analyses. A new data analysis software library was built that allows physicists to automate routine linear accelerator quality assurance tests. The package is open source, code tested, and benchmarked. Methods: Images and data were generated on a TrueBeam linac for the following routine QA tests: VMAT, starshot, CBCT, machine logs, Winston Lutz, and picket fence. The analysis library was built using the general programming language Python. Each test was analyzed with the library algorithms and compared to manual measurements taken at the timemore » of acquisition. Results: VMAT QA results agreed within 0.1% between the library and manual measurements. Machine logs (dynalogs & trajectory logs) were successfully parsed; mechanical axis positions were verified for accuracy and MLC fluence agreed well with EPID measurements. CBCT QA measurements were within 10 HU and 0.2mm where applicable. Winston Lutz isocenter size measurements were within 0.2mm of TrueBeam’s Machine Performance Check. Starshot analysis was within 0.2mm of the Winston Lutz results for the same conditions. Picket fence images with and without a known error showed that the library was capable of detecting MLC offsets within 0.02mm. Conclusion: A new routine QA software library has been benchmarked and is available for use by the community. The library is open-source and extensible for use in larger systems.« less

Knowledge-Based Aircraft Automation: Managers Guide on the use of Artificial Intelligence for Aircraft Automation and Verification and Validation Approach for a Neural-Based Flight Controller

NASA Technical Reports Server (NTRS)

Broderick, Ron

1997-01-01

The ultimate goal of this report was to integrate the powerful tools of artificial intelligence into the traditional process of software development. To maintain the US aerospace competitive advantage, traditional aerospace and software engineers need to more easily incorporate the technology of artificial intelligence into the advanced aerospace systems being designed today. The future goal was to transition artificial intelligence from an emerging technology to a standard technology that is considered early in the life cycle process to develop state-of-the-art aircraft automation systems. This report addressed the future goal in two ways. First, it provided a matrix that identified typical aircraft automation applications conducive to various artificial intelligence methods. The purpose of this matrix was to provide top-level guidance to managers contemplating the possible use of artificial intelligence in the development of aircraft automation. Second, the report provided a methodology to formally evaluate neural networks as part of the traditional process of software development. The matrix was developed by organizing the discipline of artificial intelligence into the following six methods: logical, object representation-based, distributed, uncertainty management, temporal and neurocomputing. Next, a study of existing aircraft automation applications that have been conducive to artificial intelligence implementation resulted in the following five categories: pilot-vehicle interface, system status and diagnosis, situation assessment, automatic flight planning, and aircraft flight control. The resulting matrix provided management guidance to understand artificial intelligence as it applied to aircraft automation. The approach taken to develop a methodology to formally evaluate neural networks as part of the software engineering life cycle was to start with the existing software quality assurance standards and to change these standards to include neural network development. The changes were to include evaluation tools that can be applied to neural networks at each phase of the software engineering life cycle. The result was a formal evaluation approach to increase the product quality of systems that use neural networks for their implementation.

CT colonography: automated measurement of colonic polyps compared with manual techniques--human in vitro study.

PubMed

Taylor, Stuart A; Slater, Andrew; Halligan, Steve; Honeyfield, Lesley; Roddie, Mary E; Demeshski, Jamshid; Amin, Hamdam; Burling, David

2007-01-01

To prospectively investigate the relative accuracy and reproducibility of manual and automated computer software measurements by using polyps of known size in a human colectomy specimen. Institutional review board approval was obtained for the study; written consent for use of the surgical specimen was obtained. A colectomy specimen containing 27 polyps from a 16-year-old male patient with familial adenomatous polyposis was insufflated, submerged in a container with solution, and scanned at four-section multi-detector row computed tomography (CT). A histopathologist measured the maximum dimension of all polyps in the opened specimen. Digital photographs and line drawings were produced to aid CT-histologic measurement correlation. A novice (radiographic technician) and an experienced (radiologist) observer independently estimated polyp diameter with three methods: manual two-dimensional (2D) and manual three-dimensional (3D) measurement with software calipers and automated measurement with software (automatic). Data were analyzed with paired t tests and Bland-Altman limits of agreement. Seven polyps (

Behavior-dependent Routing: Responding to Anomalies with Automated Low-cost Measures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oehmen, Christopher S.; Carroll, Thomas E.; Paulson, Patrick R.

2015-10-12

This is a conference paper submission describing research and software implementation of a cybersecurity concept that uses behavior models to trigger changes in routing of network traffic. As user behavior deviates more and more from baseline models, traffic is routed through more elevated layers of analysis and control.

Problem Solving Techniques for the Design of Algorithms.

ERIC Educational Resources Information Center

Kant, Elaine; Newell, Allen

1984-01-01

Presents model of algorithm design (activity in software development) based on analysis of protocols of two subjects designing three convex hull algorithms. Automation methods, methods for studying algorithm design, role of discovery in problem solving, and comparison of different designs of case study according to model are highlighted.…

Flight Experiment Demonstration System (FEDS) analysis report

NASA Technical Reports Server (NTRS)

Shank, D. E.

1986-01-01

The purpose of the Flight Experiment Demonstration System (FEDS) was to show, in a simulated spacecraft environment, the feasibility of using a microprocessor to automate the onboard orbit determination functions. The software and hardware configuration used to support FEDS during the demonstration and the results of the demonstration are discussed.

Advanced space system analysis software. Technical, user, and programmer guide

NASA Technical Reports Server (NTRS)

Farrell, C. E.; Zimbelman, H. F.

1981-01-01

The LASS computer program provides a tool for interactive preliminary and conceptual design of LSS. Eight program modules were developed, including four automated model geometry generators, an associated mass properties module, an appendage synthesizer module, an rf analysis module, and an orbital transfer analysis module. The existing rigid body controls analysis module was modified to permit analysis of effects of solar pressure on orbital performance. A description of each module, user instructions, and programmer information are included.

Oufti: An integrated software package for high-accuracy, high-throughput quantitative microscopy analysis

PubMed Central

Paintdakhi, Ahmad; Parry, Bradley; Campos, Manuel; Irnov, Irnov; Elf, Johan; Surovtsev, Ivan; Jacobs-Wagner, Christine

2016-01-01

Summary With the realization that bacteria display phenotypic variability among cells and exhibit complex subcellular organization critical for cellular function and behavior, microscopy has re-emerged as a primary tool in bacterial research during the last decade. However, the bottleneck in today’s single-cell studies is quantitative image analysis of cells and fluorescent signals. Here, we address current limitations through the development of Oufti, a stand-alone, open-source software package for automated measurements of microbial cells and fluorescence signals from microscopy images. Oufti provides computational solutions for tracking touching cells in confluent samples, handles various cell morphologies, offers algorithms for quantitative analysis of both diffraction and non-diffraction-limited fluorescence signals, and is scalable for high-throughput analysis of massive datasets, all with subpixel precision. All functionalities are integrated in a single package. The graphical user interface, which includes interactive modules for segmentation, image analysis, and post-processing analysis, makes the software broadly accessible to users irrespective of their computational skills. PMID:26538279

Development of advanced fermentor control applications for use in an industrial automation environment.

PubMed

Hamilton, Ryan; Tamminana, Krishna; Boyd, John; Sasaki, Gen; Toda, Alex; Haskell, Sid; Danbe, Elizabeth

2013-04-01

We present a software platform developed by Genentech and MathWorks Consulting Group that allows arbitrary MATLAB (MATLAB is a registered trademark of The MathWorks, Inc.) functions to perform supervisory control of process equipment (in this case, fermentors) via the OLE for process control (OPC) communication protocol, under the direction of an industrial automation layer. The software features automated synchronization and deployment of server control code and has been proven to be tolerant of OPC communication interruptions. Since deployment in the spring of 2010, this software has successfully performed supervisory control of more than 700 microbial fermentations in the Genentech pilot plant and has enabled significant reductions in the time required to develop and implement novel control strategies (months reduced to days). The software is available for download at the MathWorks File Exchange Web site at http://www.mathworks.com/matlabcentral/fileexchange/36866.

Automating spectral measurements

NASA Astrophysics Data System (ADS)

Goldstein, Fred T.

2008-09-01

This paper discusses the architecture of software utilized in spectroscopic measurements. As optical coatings become more sophisticated, there is mounting need to automate data acquisition (DAQ) from spectrophotometers. Such need is exacerbated when 100% inspection is required, ancillary devices are utilized, cost reduction is crucial, or security is vital. While instrument manufacturers normally provide point-and-click DAQ software, an application programming interface (API) may be missing. In such cases automation is impossible or expensive. An API is typically provided in libraries (*.dll, *.ocx) which may be embedded in user-developed applications. Users can thereby implement DAQ automation in several Windows languages. Another possibility, developed by FTG as an alternative to instrument manufacturers' software, is the ActiveX application (*.exe). ActiveX, a component of many Windows applications, provides means for programming and interoperability. This architecture permits a point-and-click program to act as automation client and server. Excel, for example, can control and be controlled by DAQ applications. Most importantly, ActiveX permits ancillary devices such as barcode readers and XY-stages to be easily and economically integrated into scanning procedures. Since an ActiveX application has its own user-interface, it can be independently tested. The ActiveX application then runs (visibly or invisibly) under DAQ software control. Automation capabilities are accessed via a built-in spectro-BASIC language with industry-standard (VBA-compatible) syntax. Supplementing ActiveX, spectro-BASIC also includes auxiliary serial port commands for interfacing programmable logic controllers (PLC). A typical application is automatic filter handling.

Automated face detection for occurrence and occupancy estimation in chimpanzees.

PubMed

Crunchant, Anne-Sophie; Egerer, Monika; Loos, Alexander; Burghardt, Tilo; Zuberbühler, Klaus; Corogenes, Katherine; Leinert, Vera; Kulik, Lars; Kühl, Hjalmar S

2017-03-01

Surveying endangered species is necessary to evaluate conservation effectiveness. Camera trapping and biometric computer vision are recent technological advances. They have impacted on the methods applicable to field surveys and these methods have gained significant momentum over the last decade. Yet, most researchers inspect footage manually and few studies have used automated semantic processing of video trap data from the field. The particular aim of this study is to evaluate methods that incorporate automated face detection technology as an aid to estimate site use of two chimpanzee communities based on camera trapping. As a comparative baseline we employ traditional manual inspection of footage. Our analysis focuses specifically on the basic parameter of occurrence where we assess the performance and practical value of chimpanzee face detection software. We found that the semi-automated data processing required only 2-4% of the time compared to the purely manual analysis. This is a non-negligible increase in efficiency that is critical when assessing the feasibility of camera trap occupancy surveys. Our evaluations suggest that our methodology estimates the proportion of sites used relatively reliably. Chimpanzees are mostly detected when they are present and when videos are filmed in high-resolution: the highest recall rate was 77%, for a false alarm rate of 2.8% for videos containing only chimpanzee frontal face views. Certainly, our study is only a first step for transferring face detection software from the lab into field application. Our results are promising and indicate that the current limitation of detecting chimpanzees in camera trap footage due to lack of suitable face views can be easily overcome on the level of field data collection, that is, by the combined placement of multiple high-resolution cameras facing reverse directions. This will enable to routinely conduct chimpanzee occupancy surveys based on camera trapping and semi-automated processing of footage. Using semi-automated ape face detection technology for processing camera trap footage requires only 2-4% of the time compared to manual analysis and allows to estimate site use by chimpanzees relatively reliably. © 2017 Wiley Periodicals, Inc.

Composable Framework Support for Software-FMEA Through Model Execution

NASA Astrophysics Data System (ADS)

Kocsis, Imre; Patricia, Andras; Brancati, Francesco; Rossi, Francesco

2016-08-01

Performing Failure Modes and Effect Analysis (FMEA) during software architecture design is becoming a basic requirement in an increasing number of domains; however, due to the lack of standardized early design phase model execution, classic SW-FMEA approaches carry significant risks and are human effort-intensive even in processes that use Model-Driven Engineering.Recently, modelling languages with standardized executable semantics have emerged. Building on earlier results, this paper describes framework support for generating executable error propagation models from such models during software architecture design. The approach carries the promise of increased precision, decreased risk and more automated execution for SW-FMEA during dependability- critical system development.

Comparison of manual & automated analysis methods for corneal endothelial cell density measurements by specular microscopy.

PubMed

Huang, Jianyan; Maram, Jyotsna; Tepelus, Tudor C; Modak, Cristina; Marion, Ken; Sadda, SriniVas R; Chopra, Vikas; Lee, Olivia L

2017-08-07

To determine the reliability of corneal endothelial cell density (ECD) obtained by automated specular microscopy versus that of validated manual methods and factors that predict such reliability. Sharp central images from 94 control and 106 glaucomatous eyes were captured with Konan specular microscope NSP-9900. All images were analyzed by trained graders using Konan CellChek Software, employing the fully- and semi-automated methods as well as Center Method. Images with low cell count (input cells number <100) and/or guttata were compared with the Center and Flex-Center Methods. ECDs were compared and absolute error was used to assess variation. The effect on ECD of age, cell count, cell size, and cell size variation was evaluated. No significant difference was observed between the Center and Flex-Center Methods in corneas with guttata (p=0.48) or low ECD (p=0.11). No difference (p=0.32) was observed in ECD of normal controls <40 yrs old between the fully-automated method and manual Center Method. However, in older controls and glaucomatous eyes, ECD was overestimated by the fully-automated method (p=0.034) and semi-automated method (p=0.025) as compared to manual method. Our findings show that automated analysis significantly overestimates ECD in the eyes with high polymegathism and/or large cell size, compared to the manual method. Therefore, we discourage reliance upon the fully-automated method alone to perform specular microscopy analysis, particularly if an accurate ECD value is imperative. Copyright © 2017. Published by Elsevier España, S.L.U.

Development and Evaluation of a Measure of Library Automation.

ERIC Educational Resources Information Center

Pungitore, Verna L.

1986-01-01

Construct validity and reliability estimates indicate that study designed to measure utilization of automation in public and academic libraries was successful in tentatively identifying and measuring three subdimensions of level of automation: quality of hardware, method of software development, and number of automation specialists. Questionnaire…

Cardiac imaging: working towards fully-automated machine analysis & interpretation.

PubMed

Slomka, Piotr J; Dey, Damini; Sitek, Arkadiusz; Motwani, Manish; Berman, Daniel S; Germano, Guido

2017-03-01

Non-invasive imaging plays a critical role in managing patients with cardiovascular disease. Although subjective visual interpretation remains the clinical mainstay, quantitative analysis facilitates objective, evidence-based management, and advances in clinical research. This has driven developments in computing and software tools aimed at achieving fully automated image processing and quantitative analysis. In parallel, machine learning techniques have been used to rapidly integrate large amounts of clinical and quantitative imaging data to provide highly personalized individual patient-based conclusions. Areas covered: This review summarizes recent advances in automated quantitative imaging in cardiology and describes the latest techniques which incorporate machine learning principles. The review focuses on the cardiac imaging techniques which are in wide clinical use. It also discusses key issues and obstacles for these tools to become utilized in mainstream clinical practice. Expert commentary: Fully-automated processing and high-level computer interpretation of cardiac imaging are becoming a reality. Application of machine learning to the vast amounts of quantitative data generated per scan and integration with clinical data also facilitates a move to more patient-specific interpretation. These developments are unlikely to replace interpreting physicians but will provide them with highly accurate tools to detect disease, risk-stratify, and optimize patient-specific treatment. However, with each technological advance, we move further from human dependence and closer to fully-automated machine interpretation.

Automated Microflow NMR: Routine Analysis of Five-Microliter Samples

PubMed Central

Jansma, Ariane; Chuan, Tiffany; Geierstanger, Bernhard H.; Albrecht, Robert W.; Olson, Dean L.; Peck, Timothy L.

2006-01-01

A microflow CapNMR probe double-tuned for 1H and 13C was installed on a 400-MHz NMR spectrometer and interfaced to an automated liquid handler. Individual samples dissolved in DMSO-d6 are submitted for NMR analysis in vials containing as little as 10 μL of sample. Sets of samples are submitted in a low-volume 384-well plate. Of the 10 μL of sample per well, as with vials, 5 μL is injected into the microflow NMR probe for analysis. For quality control of chemical libraries, 1D NMR spectra are acquired under full automation from 384-well plates on as many as 130 compounds within 24 h using 128 scans per spectrum and a sample-to-sample cycle time of ∼11 min. Because of the low volume requirements and high mass sensitivity of the microflow NMR system, 30 nmol of a typical small molecule is sufficient to obtain high-quality, well-resolved, 1D proton or 2D COSY NMR spectra in ∼6 or 20 min of data acquisition time per experiment, respectively. Implementation of pulse programs with automated solvent peak identification and suppression allow for reliable data collection, even for samples submitted in fully protonated DMSO. The automated microflow NMR system is controlled and monitored using web-based software. PMID:16194121

Automated real-time software development

NASA Technical Reports Server (NTRS)

Jones, Denise R.; Walker, Carrie K.; Turkovich, John J.

1993-01-01

A Computer-Aided Software Engineering (CASE) system has been developed at the Charles Stark Draper Laboratory (CSDL) under the direction of the NASA Langley Research Center. The CSDL CASE tool provides an automated method of generating source code and hard copy documentation from functional application engineering specifications. The goal is to significantly reduce the cost of developing and maintaining real-time scientific and engineering software while increasing system reliability. This paper describes CSDL CASE and discusses demonstrations that used the tool to automatically generate real-time application code.

The Automated Programming of Electronic Displays.

DTIC Science & Technology

1986-09-01

A182 931 THE AUTOMATED PROGRAMMING OF ELECTRONIC DISPLAYSCU) 11 SOFTWARE CONSULTING SPECIALIST INC FORT MAYNE IN R W HASKER ET AL SEP 86 AFURL-TR-86...M. R. Fritsch Software Consulting Specialists , Inc. ( P. 0. Box 15367 O Fort Wayne, IN 46885 00 V September 1986 S Final Report for Period July 1985...N 05 111 0 PRO~l S AGRAM CL(CWfT.P^OJ(CV. TASK Software Consulting Specialists , Inc. ;Ms CA 01 Wol WUNSCAS P. 0. Box 15367 62201F Fort Wayne, IN

Final Report Ra Power Management 1255 10-15-16 FINAL_Public

DOE Office of Scientific and Technical Information (OSTI.GOV)

Iverson, Aaron

Ra Power Management (RPM) has developed a cloud based software platform that manages the financial and operational functions of third party financed solar projects throughout their lifecycle. RPM’s software streamlines and automates the sales, financing, and management of a portfolio of solar assets. The software helps solar developers automate the most difficult aspects of asset management, leading to increased transparency, efficiency, and reduction in human error. More importantly, our platform will help developers save money by improving their operating margins

KCNSC Automated RAIL

DOE Office of Scientific and Technical Information (OSTI.GOV)

Branson, Donald

The KCNSC Automated RAIL (Rolling Action Item List) system provides an electronic platform to manage and escalate rolling action items within an business and manufacturing environment at Honeywell. The software enables a tiered approach to issue management where issues are escalated up a management chain based on team input and compared to business metrics. The software manages action items at different levels of the organization and allows all users to discuss action items concurrently. In addition, the software drives accountability through timely emails and proper visibility during team meetings.

Automated analysis of time-lapse fluorescence microscopy images: from live cell images to intracellular foci.

PubMed

Dzyubachyk, Oleh; Essers, Jeroen; van Cappellen, Wiggert A; Baldeyron, Céline; Inagaki, Akiko; Niessen, Wiro J; Meijering, Erik

2010-10-01

Complete, accurate and reproducible analysis of intracellular foci from fluorescence microscopy image sequences of live cells requires full automation of all processing steps involved: cell segmentation and tracking followed by foci segmentation and pattern analysis. Integrated systems for this purpose are lacking. Extending our previous work in cell segmentation and tracking, we developed a new system for performing fully automated analysis of fluorescent foci in single cells. The system was validated by applying it to two common tasks: intracellular foci counting (in DNA damage repair experiments) and cell-phase identification based on foci pattern analysis (in DNA replication experiments). Experimental results show that the system performs comparably to expert human observers. Thus, it may replace tedious manual analyses for the considered tasks, and enables high-content screening. The described system was implemented in MATLAB (The MathWorks, Inc., USA) and compiled to run within the MATLAB environment. The routines together with four sample datasets are available at http://celmia.bigr.nl/. The software is planned for public release, free of charge for non-commercial use, after publication of this article.

CalQuo: automated, simultaneous single-cell and population-level quantification of global intracellular Ca2+ responses.

PubMed

Fritzsche, Marco; Fernandes, Ricardo A; Colin-York, Huw; Santos, Ana M; Lee, Steven F; Lagerholm, B Christoffer; Davis, Simon J; Eggeling, Christian

2015-11-13

Detecting intracellular calcium signaling with fluorescent calcium indicator dyes is often coupled with microscopy techniques to follow the activation state of non-excitable cells, including lymphocytes. However, the analysis of global intracellular calcium responses both at the single-cell level and in large ensembles simultaneously has yet to be automated. Here, we present a new software package, CalQuo (Calcium Quantification), which allows the automated analysis and simultaneous monitoring of global fluorescent calcium reporter-based signaling responses in up to 1000 single cells per experiment, at temporal resolutions of sub-seconds to seconds. CalQuo quantifies the number and fraction of responding cells, the temporal dependence of calcium signaling and provides global and individual calcium-reporter fluorescence intensity profiles. We demonstrate the utility of the new method by comparing the calcium-based signaling responses of genetically manipulated human lymphocytic cell lines.

Autogen Version 2.0

NASA Technical Reports Server (NTRS)

Gladden, Roy

2007-01-01

Version 2.0 of the autogen software has been released. "Autogen" (automated sequence generation) signifies both a process and software used to implement the process of automated generation of sequences of commands in a standard format for uplink to spacecraft. Autogen requires fewer workers than are needed for older manual sequence-generation processes and reduces sequence-generation times from weeks to minutes.

Automating Reference Desk Files with Microcomputers in a Public Library: An Exploration of Data Resources, Methods, and Software.

ERIC Educational Resources Information Center

Miley, David W.

Many reference librarians still rely on manual searches to access vertical files, ready reference files, and other information stored in card files, drawers, and notebooks scattered around the reference department. Automated access to these materials via microcomputers using database management software may speed up the process. This study focuses…

Applying formal methods and object-oriented analysis to existing flight software

NASA Technical Reports Server (NTRS)

Cheng, Betty H. C.; Auernheimer, Brent

1993-01-01

Correctness is paramount for safety-critical software control systems. Critical software failures in medical radiation treatment, communications, and defense are familiar to the public. The significant quantity of software malfunctions regularly reported to the software engineering community, the laws concerning liability, and a recent NRC Aeronautics and Space Engineering Board report additionally motivate the use of error-reducing and defect detection software development techniques. The benefits of formal methods in requirements driven software development ('forward engineering') is well documented. One advantage of rigorously engineering software is that formal notations are precise, verifiable, and facilitate automated processing. This paper describes the application of formal methods to reverse engineering, where formal specifications are developed for a portion of the shuttle on-orbit digital autopilot (DAP). Three objectives of the project were to: demonstrate the use of formal methods on a shuttle application, facilitate the incorporation and validation of new requirements for the system, and verify the safety-critical properties to be exhibited by the software.

Design and validation of Segment--freely available software for cardiovascular image analysis.

PubMed

Heiberg, Einar; Sjögren, Jane; Ugander, Martin; Carlsson, Marcus; Engblom, Henrik; Arheden, Håkan

2010-01-11

Commercially available software for cardiovascular image analysis often has limited functionality and frequently lacks the careful validation that is required for clinical studies. We have already implemented a cardiovascular image analysis software package and released it as freeware for the research community. However, it was distributed as a stand-alone application and other researchers could not extend it by writing their own custom image analysis algorithms. We believe that the work required to make a clinically applicable prototype can be reduced by making the software extensible, so that researchers can develop their own modules or improvements. Such an initiative might then serve as a bridge between image analysis research and cardiovascular research. The aim of this article is therefore to present the design and validation of a cardiovascular image analysis software package (Segment) and to announce its release in a source code format. Segment can be used for image analysis in magnetic resonance imaging (MRI), computed tomography (CT), single photon emission computed tomography (SPECT) and positron emission tomography (PET). Some of its main features include loading of DICOM images from all major scanner vendors, simultaneous display of multiple image stacks and plane intersections, automated segmentation of the left ventricle, quantification of MRI flow, tools for manual and general object segmentation, quantitative regional wall motion analysis, myocardial viability analysis and image fusion tools. Here we present an overview of the validation results and validation procedures for the functionality of the software. We describe a technique to ensure continued accuracy and validity of the software by implementing and using a test script that tests the functionality of the software and validates the output. The software has been made freely available for research purposes in a source code format on the project home page http://segment.heiberg.se. Segment is a well-validated comprehensive software package for cardiovascular image analysis. It is freely available for research purposes provided that relevant original research publications related to the software are cited.

Large Scale Screening of Low Cost Ferritic Steel Designs For Advanced Ultra Supercritical Boiler Using First Principles Methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ouyang, Lizhi

Advanced Ultra Supercritical Boiler (AUSC) requires materials that can operate in corrosive environment at temperature and pressure as high as 760°C (or 1400°F) and 5000psi, respectively, while at the same time maintain good ductility at low temperature. We develop automated simulation software tools to enable fast large scale screening studies of candidate designs. While direct evaluation of creep rupture strength and ductility are currently not feasible, properties such as energy, elastic constants, surface energy, interface energy, and stack fault energy can be used to assess their relative ductility and creeping strength. We implemented software to automate the complex calculations tomore » minimize human inputs in the tedious screening studies which involve model structures generation, settings for first principles calculations, results analysis and reporting. The software developed in the project and library of computed mechanical properties of phases found in ferritic steels, many are complex solid solutions estimated for the first time, will certainly help the development of low cost ferritic steel for AUSC.« less

Towards automated traceability maintenance

PubMed Central

Mäder, Patrick; Gotel, Orlena

2012-01-01

Traceability relations support stakeholders in understanding the dependencies between artifacts created during the development of a software system and thus enable many development-related tasks. To ensure that the anticipated benefits of these tasks can be realized, it is necessary to have an up-to-date set of traceability relations between the established artifacts. This goal requires the creation of traceability relations during the initial development process. Furthermore, the goal also requires the maintenance of traceability relations over time as the software system evolves in order to prevent their decay. In this paper, an approach is discussed that supports the (semi-) automated update of traceability relations between requirements, analysis and design models of software systems expressed in the UML. This is made possible by analyzing change events that have been captured while working within a third-party UML modeling tool. Within the captured flow of events, development activities comprised of several events are recognized. These are matched with predefined rules that direct the update of impacted traceability relations. The overall approach is supported by a prototype tool and empirical results on the effectiveness of tool-supported traceability maintenance are provided. PMID:23471308

Evaluation of automated decisionmaking methodologies and development of an integrated robotic system simulation

NASA Technical Reports Server (NTRS)

Haley, D. C.; Almand, B. J.; Thomas, M. M.; Krauze, L. D.; Gremban, K. D.; Sanborn, J. C.; Kelly, J. H.; Depkovich, T. M.

1984-01-01

A generic computer simulation for manipulator systems (ROBSIM) was implemented and the specific technologies necessary to increase the role of automation in various missions were developed. The specific items developed are: (1) capability for definition of a manipulator system consisting of multiple arms, load objects, and an environment; (2) capability for kinematic analysis, requirements analysis, and response simulation of manipulator motion; (3) postprocessing options such as graphic replay of simulated motion and manipulator parameter plotting; (4) investigation and simulation of various control methods including manual force/torque and active compliances control; (5) evaluation and implementation of three obstacle avoidance methods; (6) video simulation and edge detection; and (7) software simulation validation.

Land surface Verification Toolkit (LVT)

NASA Technical Reports Server (NTRS)

Kumar, Sujay V.

2017-01-01

LVT is a framework developed to provide an automated, consolidated environment for systematic land surface model evaluation Includes support for a range of in-situ, remote-sensing and other model and reanalysis products. Supports the analysis of outputs from various LIS subsystems, including LIS-DA, LIS-OPT, LIS-UE. Note: The Land Information System Verification Toolkit (LVT) is a NASA software tool designed to enable the evaluation, analysis and comparison of outputs generated by the Land Information System (LIS). The LVT software is released under the terms and conditions of the NASA Open Source Agreement (NOSA) Version 1.1 or later. Land Information System Verification Toolkit (LVT) NOSA.

TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics.

PubMed

Röst, Hannes L; Liu, Yansheng; D'Agostino, Giuseppe; Zanella, Matteo; Navarro, Pedro; Rosenberger, George; Collins, Ben C; Gillet, Ludovic; Testa, Giuseppe; Malmström, Lars; Aebersold, Ruedi

2016-09-01

Next-generation mass spectrometric (MS) techniques such as SWATH-MS have substantially increased the throughput and reproducibility of proteomic analysis, but ensuring consistent quantification of thousands of peptide analytes across multiple liquid chromatography-tandem MS (LC-MS/MS) runs remains a challenging and laborious manual process. To produce highly consistent and quantitatively accurate proteomics data matrices in an automated fashion, we developed TRIC (http://proteomics.ethz.ch/tric/), a software tool that utilizes fragment-ion data to perform cross-run alignment, consistent peak-picking and quantification for high-throughput targeted proteomics. TRIC reduced the identification error compared to a state-of-the-art SWATH-MS analysis without alignment by more than threefold at constant recall while correcting for highly nonlinear chromatographic effects. On a pulsed-SILAC experiment performed on human induced pluripotent stem cells, TRIC was able to automatically align and quantify thousands of light and heavy isotopic peak groups. Thus, TRIC fills a gap in the pipeline for automated analysis of massively parallel targeted proteomics data sets.

Evaluation of verification and testing tools for FORTRAN programs

NASA Technical Reports Server (NTRS)

Smith, K. A.

1980-01-01

Two automated software verification and testing systems were developed for use in the analysis of computer programs. An evaluation of the static analyzer DAVE and the dynamic analyzer PET, which are used in the analysis of FORTRAN programs on Control Data (CDC) computers, are described. Both systems were found to be effective and complementary, and are recommended for use in testing FORTRAN programs.

Digital Transplantation Pathology: Combining Whole Slide Imaging, Multiplex Staining, and Automated Image Analysis

PubMed Central

Isse, Kumiko; Lesniak, Andrew; Grama, Kedar; Roysam, Badrinath; Minervini, Martha I.; Demetris, Anthony J

2013-01-01

Conventional histopathology is the gold standard for allograft monitoring, but its value proposition is increasingly questioned. “-Omics” analysis of tissues, peripheral blood and fluids and targeted serologic studies provide mechanistic insights into allograft injury not currently provided by conventional histology. Microscopic biopsy analysis, however, provides valuable and unique information: a) spatial-temporal relationships; b) rare events/cells; c) complex structural context; and d) integration into a “systems” model. Nevertheless, except for immunostaining, no transformative advancements have “modernized” routine microscopy in over 100 years. Pathologists now team with hardware and software engineers to exploit remarkable developments in digital imaging, nanoparticle multiplex staining, and computational image analysis software to bridge the traditional histology - global “–omic” analyses gap. Included are side-by-side comparisons, objective biopsy finding quantification, multiplexing, automated image analysis, and electronic data and resource sharing. Current utilization for teaching, quality assurance, conferencing, consultations, research and clinical trials is evolving toward implementation for low-volume, high-complexity clinical services like transplantation pathology. Cost, complexities of implementation, fluid/evolving standards, and unsettled medical/legal and regulatory issues remain as challenges. Regardless, challenges will be overcome and these technologies will enable transplant pathologists to increase information extraction from tissue specimens and contribute to cross-platform biomarker discovery for improved outcomes. PMID:22053785

Visual Recognition Software for Binary Classification and Its Application to Spruce Pollen Identification

PubMed Central

Tcheng, David K.; Nayak, Ashwin K.; Fowlkes, Charless C.; Punyasena, Surangi W.

2016-01-01

Discriminating between black and white spruce (Picea mariana and Picea glauca) is a difficult palynological classification problem that, if solved, would provide valuable data for paleoclimate reconstructions. We developed an open-source visual recognition software (ARLO, Automated Recognition with Layered Optimization) capable of differentiating between these two species at an accuracy on par with human experts. The system applies pattern recognition and machine learning to the analysis of pollen images and discovers general-purpose image features, defined by simple features of lines and grids of pixels taken at different dimensions, size, spacing, and resolution. It adapts to a given problem by searching for the most effective combination of both feature representation and learning strategy. This results in a powerful and flexible framework for image classification. We worked with images acquired using an automated slide scanner. We first applied a hash-based “pollen spotting” model to segment pollen grains from the slide background. We next tested ARLO’s ability to reconstruct black to white spruce pollen ratios using artificially constructed slides of known ratios. We then developed a more scalable hash-based method of image analysis that was able to distinguish between the pollen of black and white spruce with an estimated accuracy of 83.61%, comparable to human expert performance. Our results demonstrate the capability of machine learning systems to automate challenging taxonomic classifications in pollen analysis, and our success with simple image representations suggests that our approach is generalizable to many other object recognition problems. PMID:26867017

An Empirical Evaluation of Automated Theorem Provers in Software Certification

NASA Technical Reports Server (NTRS)

Denney, Ewen; Fischer, Bernd; Schumann, Johann

2004-01-01

We describe a system for the automated certification of safety properties of NASA software. The system uses Hoare-style program verification technology to generate proof obligations which are then processed by an automated first-order theorem prover (ATP). We discuss the unique requirements this application places on the ATPs, focusing on automation, proof checking, and usability. For full automation, however, the obligations must be aggressively preprocessed and simplified, and we demonstrate how the individual simplification stages, which are implemented by rewriting, influence the ability of the ATPs to solve the proof tasks. Our results are based on 13 certification experiments that lead to more than 25,000 proof tasks which have each been attempted by Vampire, Spass, e-setheo, and Otter. The proofs found by Otter have been proof-checked by IVY.

Applications of pathology-assisted image analysis of immunohistochemistry-based biomarkers in oncology.

PubMed

Shinde, V; Burke, K E; Chakravarty, A; Fleming, M; McDonald, A A; Berger, A; Ecsedy, J; Blakemore, S J; Tirrell, S M; Bowman, D

2014-01-01

Immunohistochemistry-based biomarkers are commonly used to understand target inhibition in key cancer pathways in preclinical models and clinical studies. Automated slide-scanning and advanced high-throughput image analysis software technologies have evolved into a routine methodology for quantitative analysis of immunohistochemistry-based biomarkers. Alongside the traditional pathology H-score based on physical slides, the pathology world is welcoming digital pathology and advanced quantitative image analysis, which have enabled tissue- and cellular-level analysis. An automated workflow was implemented that includes automated staining, slide-scanning, and image analysis methodologies to explore biomarkers involved in 2 cancer targets: Aurora A and NEDD8-activating enzyme (NAE). The 2 workflows highlight the evolution of our immunohistochemistry laboratory and the different needs and requirements of each biological assay. Skin biopsies obtained from MLN8237 (Aurora A inhibitor) phase 1 clinical trials were evaluated for mitotic and apoptotic index, while mitotic index and defects in chromosome alignment and spindles were assessed in tumor biopsies to demonstrate Aurora A inhibition. Additionally, in both preclinical xenograft models and an acute myeloid leukemia phase 1 trial of the NAE inhibitor MLN4924, development of a novel image algorithm enabled measurement of downstream pathway modulation upon NAE inhibition. In the highlighted studies, developing a biomarker strategy based on automated image analysis solutions enabled project teams to confirm target and pathway inhibition and understand downstream outcomes of target inhibition with increased throughput and quantitative accuracy. These case studies demonstrate a strategy that combines a pathologist's expertise with automated image analysis to support oncology drug discovery and development programs.

Information Extraction for System-Software Safety Analysis: Calendar Year 2008 Year-End Report

NASA Technical Reports Server (NTRS)

Malin, Jane T.

2009-01-01

This annual report describes work to integrate a set of tools to support early model-based analysis of failures and hazards due to system-software interactions. The tools perform and assist analysts in the following tasks: 1) extract model parts from text for architecture and safety/hazard models; 2) combine the parts with library information to develop the models for visualization and analysis; 3) perform graph analysis and simulation to identify and evaluate possible paths from hazard sources to vulnerable entities and functions, in nominal and anomalous system-software configurations and scenarios; and 4) identify resulting candidate scenarios for software integration testing. There has been significant technical progress in model extraction from Orion program text sources, architecture model derivation (components and connections) and documentation of extraction sources. Models have been derived from Internal Interface Requirements Documents (IIRDs) and FMEA documents. Linguistic text processing is used to extract model parts and relationships, and the Aerospace Ontology also aids automated model development from the extracted information. Visualizations of these models assist analysts in requirements overview and in checking consistency and completeness.

Web based aphasia test using service oriented architecture (SOA)

NASA Astrophysics Data System (ADS)

Voos, J. A.; Vigliecca, N. S.; Gonzalez, E. A.

2007-11-01

Based on an aphasia test for Spanish speakers which analyze the patient's basic resources of verbal communication, a web-enabled software was developed to automate its execution. A clinical database was designed as a complement, in order to evaluate the antecedents (risk factors, pharmacological and medical backgrounds, neurological or psychiatric symptoms, brain injury -anatomical and physiological characteristics, etc) which are necessary to carry out a multi-factor statistical analysis in different samples of patients. The automated test was developed following service oriented architecture and implemented in a web site which contains a tests suite, which would allow both integrating the aphasia test with other neuropsychological instruments and increasing the available site information for scientific research. The test design, the database and the study of its psychometric properties (validity, reliability and objectivity) were made in conjunction with neuropsychological researchers, who participate actively in the software design, based on the patients or other subjects of investigation feedback.

Robust binarization of degraded document images using heuristics

NASA Astrophysics Data System (ADS)

Parker, Jon; Frieder, Ophir; Frieder, Gideon

2013-12-01

Historically significant documents are often discovered with defects that make them difficult to read and analyze. This fact is particularly troublesome if the defects prevent software from performing an automated analysis. Image enhancement methods are used to remove or minimize document defects, improve software performance, and generally make images more legible. We describe an automated, image enhancement method that is input page independent and requires no training data. The approach applies to color or greyscale images with hand written script, typewritten text, images, and mixtures thereof. We evaluated the image enhancement method against the test images provided by the 2011 Document Image Binarization Contest (DIBCO). Our method outperforms all 2011 DIBCO entrants in terms of average F1 measure - doing so with a significantly lower variance than top contest entrants. The capability of the proposed method is also illustrated using select images from a collection of historic documents stored at Yad Vashem Holocaust Memorial in Israel.

An overview of suite for automated global electronic biosurveillance (SAGES)

NASA Astrophysics Data System (ADS)

Lewis, Sheri L.; Feighner, Brian H.; Loschen, Wayne A.; Wojcik, Richard A.; Skora, Joseph F.; Coberly, Jacqueline S.; Blazes, David L.

2012-06-01

Public health surveillance is undergoing a revolution driven by advances in the field of information technology. Many countries have experienced vast improvements in the collection, ingestion, analysis, visualization, and dissemination of public health data. Resource-limited countries have lagged behind due to challenges in information technology infrastructure, public health resources, and the costs of proprietary software. The Suite for Automated Global Electronic bioSurveillance (SAGES) is a collection of modular, flexible, freely-available software tools for electronic disease surveillance in resource-limited settings. One or more SAGES tools may be used in concert with existing surveillance applications or the SAGES tools may be used en masse for an end-to-end biosurveillance capability. This flexibility allows for the development of an inexpensive, customized, and sustainable disease surveillance system. The ability to rapidly assess anomalous disease activity may lead to more efficient use of limited resources and better compliance with World Health Organization International Health Regulations.

Support for life-cycle product reuse in NASA's SSE

NASA Technical Reports Server (NTRS)

Shotton, Charles

1989-01-01

The Software Support Environment (SSE) is a software factory for the production of Space Station Freedom Program operational software. The SSE is to be centrally developed and maintained and used to configure software production facilities in the field. The PRC product TTCQF provides for an automated qualification process and analysis of existing code that can be used for software reuse. The interrogation subsystem permits user queries of the reusable data and components which have been identified by an analyzer and qualified with associated metrics. The concept includes reuse of non-code life-cycle components such as requirements and designs. Possible types of reusable life-cycle components include templates, generics, and as-is items. Qualification of reusable elements requires analysis (separation of candidate components into primitives), qualification (evaluation of primitives for reusability according to reusability criteria) and loading (placing qualified elements into appropriate libraries). There can be different qualifications for different installations, methodologies, applications and components. Identifying reusable software and related components is labor-intensive and is best carried out as an integrated function of an SSE.

A Sidekick for Membrane Simulations: Automated Ensemble Molecular Dynamics Simulations of Transmembrane Helices

PubMed Central

Hall, Benjamin A; Halim, Khairul Abd; Buyan, Amanda; Emmanouil, Beatrice; Sansom, Mark S P

2016-01-01

The interactions of transmembrane (TM) α-helices with the phospholipid membrane and with one another are central to understanding the structure and stability of integral membrane proteins. These interactions may be analysed via coarse-grained molecular dynamics (CGMD) simulations. To obtain statistically meaningful analysis of TM helix interactions, large (N ca. 100) ensembles of CGMD simulations are needed. To facilitate the running and analysis of such ensembles of simulations we have developed Sidekick, an automated pipeline software for performing high throughput CGMD simulations of α-helical peptides in lipid bilayer membranes. Through an end-to-end approach, which takes as input a helix sequence and outputs analytical metrics derived from CGMD simulations, we are able to predict the orientation and likelihood of insertion into a lipid bilayer of a given helix of family of helix sequences. We illustrate this software via analysis of insertion into a membrane of short hydrophobic TM helices containing a single cationic arginine residue positioned at different positions along the length of the helix. From analysis of these ensembles of simulations we estimate apparent energy barriers to insertion which are comparable to experimentally determined values. In a second application we use CGMD simulations to examine self-assembly of dimers of TM helices from the ErbB1 receptor tyrosine kinase, and analyse the numbers of simulation repeats necessary to obtain convergence of simple descriptors of the mode of packing of the two helices within a dimer. Our approach offers proof-of-principle platform for the further employment of automation in large ensemble CGMD simulations of membrane proteins. PMID:26580541

Automated analysis of calcium spiking profiles with CaSA software: two case studies from root-microbe symbioses

PubMed Central

2013-01-01

Background Repeated oscillations in intracellular calcium (Ca2+) concentration, known as Ca2+ spiking signals, have been described in plants for a limited number of cellular responses to biotic or abiotic stimuli and most notably the common symbiotic signaling pathway (CSSP) which mediates the recognition by their plant hosts of two endosymbiotic microbes, arbuscular mycorrhizal (AM) fungi and nitrogen fixing rhizobia. The detailed analysis of the complexity and variability of the Ca2+ spiking patterns which have been revealed in recent studies requires both extensive datasets and sophisticated statistical tools. Results As a contribution, we have developed automated Ca2+ spiking analysis (CaSA) software that performs i) automated peak detection, ii) statistical analyses based on the detected peaks, iii) autocorrelation analysis of peak-to-peak intervals to highlight major traits in the spiking pattern. We have evaluated CaSA in two experimental studies. In the first, CaSA highlighted unpredicted differences in the spiking patterns induced in Medicago truncatula root epidermal cells by exudates of the AM fungus Gigaspora margarita as a function of the phosphate concentration in the growth medium of both host and fungus. In the second study we compared the spiking patterns triggered by either AM fungal or rhizobial symbiotic signals. CaSA revealed the existence of different patterns in signal periodicity, which are thought to contribute to the so-called Ca2+ signature. Conclusions We therefore propose CaSA as a useful tool for characterizing oscillatory biological phenomena such as Ca2+ spiking. PMID:24369773

A LabVIEW based template for user created experiment automation.

PubMed

Kim, D J; Fisk, Z

2012-12-01

We have developed an expandable software template to automate user created experiments. The LabVIEW based template is easily modifiable to add together user created measurements, controls, and data logging with virtually any type of laboratory equipment. We use reentrant sequential selection to implement sequence script making it possible to wrap a long series of the user created experiments and execute them in sequence. Details of software structure and application examples for scanning probe microscope and automated transport experiments using custom built laboratory electronics and a cryostat are described.

DOE Office of Scientific and Technical Information (OSTI.GOV)

White, Amanda M.; Daly, Don S.; Willse, Alan R.

The Automated Microarray Image Analysis (AMIA) Toolbox for MATLAB is a flexible, open-source microarray image analysis tool that allows the user to customize analysis of sets of microarray images. This tool provides several methods of identifying and quantify spot statistics, as well as extensive diagnostic statistics and images to identify poor data quality or processing. The open nature of this software allows researchers to understand the algorithms used to provide intensity estimates and to modify them easily if desired.

Improved accuracy in ground-based facilities - Development of an automated film-reading system for ballistic ranges

NASA Technical Reports Server (NTRS)

Yates, Leslie A.

1992-01-01

Software for an automated film-reading system that uses personal computers and digitized shadowgraphs is described. The software identifies pixels associated with fiducial-line and model images, and least-squares procedures are used to calculate the positions and orientations of the images. Automated position and orientation readings for sphere and cone models are compared to those obtained using a manual film reader. When facility calibration errors are removed from these readings, the accuracy of the automated readings is better than the pixel resolution, and it is equal to, or better than, the manual readings. The effects of film-reading and facility-calibration errors on calculated aerodynamic coefficients is discussed.

DAME: planetary-prototype drilling automation.

PubMed

Glass, B; Cannon, H; Branson, M; Hanagud, S; Paulsen, G

2008-06-01

We describe results from the Drilling Automation for Mars Exploration (DAME) project, including those of the summer 2006 tests from an Arctic analog site. The drill hardware is a hardened, evolved version of the Advanced Deep Drill by Honeybee Robotics. DAME has developed diagnostic and executive software for hands-off surface operations of the evolved version of this drill. The DAME drill automation tested from 2004 through 2006 included adaptively controlled drilling operations and the downhole diagnosis of drilling faults. It also included dynamic recovery capabilities when unexpected failures or drilling conditions were discovered. DAME has developed and tested drill automation software and hardware under stressful operating conditions during its Arctic field testing campaigns at a Mars analog site.

DAME: Planetary-Prototype Drilling Automation

NASA Astrophysics Data System (ADS)

Glass, B.; Cannon, H.; Branson, M.; Hanagud, S.; Paulsen, G.

2008-06-01

We describe results from the Drilling Automation for Mars Exploration (DAME) project, including those of the summer 2006 tests from an Arctic analog site. The drill hardware is a hardened, evolved version of the Advanced Deep Drill by Honeybee Robotics. DAME has developed diagnostic and executive software for hands-off surface operations of the evolved version of this drill. The DAME drill automation tested from 2004 through 2006 included adaptively controlled drilling operations and the downhole diagnosis of drilling faults. It also included dynamic recovery capabilities when unexpected failures or drilling conditions were discovered. DAME has developed and tested drill automation software and hardware under stressful operating conditions during its Arctic field testing campaigns at a Mars analog site.

lumpR 2.0.0: an R package facilitating landscape discretisation for hillslope-based hydrological models

NASA Astrophysics Data System (ADS)

Pilz, Tobias; Francke, Till; Bronstert, Axel

2017-08-01

The characteristics of a landscape pose essential factors for hydrological processes. Therefore, an adequate representation of the landscape of a catchment in hydrological models is vital. However, many of such models exist differing, amongst others, in spatial concept and discretisation. The latter constitutes an essential pre-processing step, for which many different algorithms along with numerous software implementations exist. In that context, existing solutions are often model specific, commercial, or depend on commercial back-end software, and allow only a limited or no workflow automation at all. Consequently, a new package for the scientific software and scripting environment R, called lumpR, was developed. lumpR employs an algorithm for hillslope-based landscape discretisation directed to large-scale application via a hierarchical multi-scale approach. The package addresses existing limitations as it is free and open source, easily extendible to other hydrological models, and the workflow can be fully automated. Moreover, it is user-friendly as the direct coupling to a GIS allows for immediate visual inspection and manual adjustment. Sufficient control is furthermore retained via parameter specification and the option to include expert knowledge. Conversely, completely automatic operation also allows for extensive analysis of aspects related to landscape discretisation. In a case study, the application of the package is presented. A sensitivity analysis of the most important discretisation parameters demonstrates its efficient workflow automation. Considering multiple streamflow metrics, the employed model proved reasonably robust to the discretisation parameters. However, parameters determining the sizes of subbasins and hillslopes proved to be more important than the others, including the number of representative hillslopes, the number of attributes employed for the lumping algorithm, and the number of sub-discretisations of the representative hillslopes.

Development and improvement of the operating diagnostics systems of NPO CKTI works for turbine of thermal and nuclear power plants

NASA Astrophysics Data System (ADS)

Kovalev, I. A.; Rakovskii, V. G.; Isakov, N. Yu.; Sandovskii, A. V.

2016-03-01

The work results on the development and improvement of the techniques, algorithms, and software-hardware of continuous operating diagnostics systems of rotating units and parts of turbine equipment state are presented. In particular, to ensure the full remote service of monitored turbine equipment using web technologies, the web version of the software of the automated systems of vibration-based diagnostics (ASVD VIDAS) was developed. The experience in the automated analysis of data obtained by ASVD VIDAS form the basis of the new algorithm of early detection of such dangerous defects as rotor deflection, crack in the rotor, and strong misalignment of supports. The program-technical complex of monitoring and measuring the deflection of medium pressure rotor (PTC) realizing this algorithm will alert the electric power plant staff during a deflection and indicate its value. This will give the opportunity to take timely measures to prevent the further extension of the defect. Repeatedly, recorded cases of full or partial destruction of shrouded shelves of rotor blades of the last stages of low-pressure cylinders of steam turbines defined the need to develop a version of the automated system of blade diagnostics (ASBD SKALA) for shrouded stages. The processing, analysis, presentation, and backup of data characterizing the mechanical state of blade device are carried out with a newly developed controller of the diagnostics system. As a result of the implementation of the works, the diagnosed parameters determining the operation security of rotating elements of equipment was expanded and the new tasks on monitoring the state of units and parts of turbines were solved. All algorithmic solutions and hardware-software implementations mentioned in the article were tested on the test benches and applied at some power plants.

DOE Office of Scientific and Technical Information (OSTI.GOV)

DiCostanzo, D; Ayan, A; Woollard, J

Purpose: To automate the daily verification of each patient’s treatment by utilizing the trajectory log files (TLs) written by the Varian TrueBeam linear accelerator while reducing the number of false positives including jaw and gantry positioning errors, that are displayed in the Treatment History tab of Varian’s Chart QA module. Methods: Small deviations in treatment parameters are difficult to detect in weekly chart checks, but may be significant in reducing delivery errors, and would be critical if detected daily. Software was developed in house to read TLs. Multiple functions were implemented within the software that allow it to operate viamore » a GUI to analyze TLs, or as a script to run on a regular basis. In order to determine tolerance levels for the scripted analysis, 15,241 TLs from seven TrueBeams were analyzed. The maximum error of each axis for each TL was written to a CSV file and statistically analyzed to determine the tolerance for each axis accessible in the TLs to flag for manual review. The software/scripts developed were tested by varying the tolerance values to ensure veracity. After tolerances were determined, multiple weeks of manual chart checks were performed simultaneously with the automated analysis to ensure validity. Results: The tolerance values for the major axis were determined to be, 0.025 degrees for the collimator, 1.0 degree for the gantry, 0.002cm for the y-jaws, 0.01cm for the x-jaws, and 0.5MU for the MU. The automated verification of treatment parameters has been in clinical use for 4 months. During that time, no errors in machine delivery of the patient treatments were found. Conclusion: The process detailed here is a viable and effective alternative to manually checking treatment parameters during weekly chart checks.« less

Evolution paths for advanced automation

NASA Technical Reports Server (NTRS)

Healey, Kathleen J.

1990-01-01

As Space Station Freedom (SSF) evolves, increased automation and autonomy will be required to meet Space Station Freedom Program (SSFP) objectives. As a precursor to the use of advanced automation within the SSFP, especially if it is to be used on SSF (e.g., to automate the operation of the flight systems), the underlying technologies will need to be elevated to a high level of readiness to ensure safe and effective operations. Ground facilities supporting the development of these flight systems -- from research and development laboratories through formal hardware and software development environments -- will be responsible for achieving these levels of technology readiness. These facilities will need to evolve support the general evolution of the SSFP. This evolution will include support for increasing the use of advanced automation. The SSF Advanced Development Program has funded a study to define evolution paths for advanced automaton within the SSFP's ground-based facilities which will enable, promote, and accelerate the appropriate use of advanced automation on-board SSF. The current capability of the test beds and facilities, such as the Software Support Environment, with regard to advanced automation, has been assessed and their desired evolutionary capabilities have been defined. Plans and guidelines for achieving this necessary capability have been constructed. The approach taken has combined indepth interviews of test beds personnel at all SSF Work Package centers with awareness of relevant state-of-the-art technology and technology insertion methodologies. Key recommendations from the study include advocating a NASA-wide task force for advanced automation, and the creation of software prototype transition environments to facilitate the incorporation of advanced automation in the SSFP.

TreeRipper web application: towards a fully automated optical tree recognition software.

PubMed

Hughes, Joseph

2011-05-20

Relationships between species, genes and genomes have been printed as trees for over a century. Whilst this may have been the best format for exchanging and sharing phylogenetic hypotheses during the 20th century, the worldwide web now provides faster and automated ways of transferring and sharing phylogenetic knowledge. However, novel software is needed to defrost these published phylogenies for the 21st century. TreeRipper is a simple website for the fully-automated recognition of multifurcating phylogenetic trees (http://linnaeus.zoology.gla.ac.uk/~jhughes/treeripper/). The program accepts a range of input image formats (PNG, JPG/JPEG or GIF). The underlying command line c++ program follows a number of cleaning steps to detect lines, remove node labels, patch-up broken lines and corners and detect line edges. The edge contour is then determined to detect the branch length, tip label positions and the topology of the tree. Optical Character Recognition (OCR) is used to convert the tip labels into text with the freely available tesseract-ocr software. 32% of images meeting the prerequisites for TreeRipper were successfully recognised, the largest tree had 115 leaves. Despite the diversity of ways phylogenies have been illustrated making the design of a fully automated tree recognition software difficult, TreeRipper is a step towards automating the digitization of past phylogenies. We also provide a dataset of 100 tree images and associated tree files for training and/or benchmarking future software. TreeRipper is an open source project licensed under the GNU General Public Licence v3.

Robust Ambiguity Estimation for an Automated Analysis of the Intensive Sessions

NASA Astrophysics Data System (ADS)

Kareinen, Niko; Hobiger, Thomas; Haas, Rüdiger

2016-12-01

Very Long Baseline Interferometry (VLBI) is a unique space-geodetic technique that can directly determine the Earth's phase of rotation, namely UT1. The daily estimates of the difference between UT1 and Coordinated Universal Time (UTC) are computed from one-hour long VLBI Intensive sessions. These sessions are essential for providing timely UT1 estimates for satellite navigation systems. To produce timely UT1 estimates, efforts have been made to completely automate the analysis of VLBI Intensive sessions. This requires automated processing of X- and S-band group delays. These data often contain an unknown number of integer ambiguities in the observed group delays. In an automated analysis with the c5++ software the standard approach in resolving the ambiguities is to perform a simplified parameter estimation using a least-squares adjustment (L2-norm minimization). We implement the robust L1-norm with an alternative estimation method in c5++. The implemented method is used to automatically estimate the ambiguities in VLBI Intensive sessions for the Kokee-Wettzell baseline. The results are compared to an analysis setup where the ambiguity estimation is computed using the L2-norm. Additionally, we investigate three alternative weighting strategies for the ambiguity estimation. The results show that in automated analysis the L1-norm resolves ambiguities better than the L2-norm. The use of the L1-norm leads to a significantly higher number of good quality UT1-UTC estimates with each of the three weighting strategies.

Quantitative semi-automated analysis of morphogenesis with single-cell resolution in complex embryos

PubMed Central

Giurumescu, Claudiu A.; Kang, Sukryool; Planchon, Thomas A.; Betzig, Eric; Bloomekatz, Joshua; Yelon, Deborah; Cosman, Pamela; Chisholm, Andrew D.

2012-01-01

A quantitative understanding of tissue morphogenesis requires description of the movements of individual cells in space and over time. In transparent embryos, such as C. elegans, fluorescently labeled nuclei can be imaged in three-dimensional time-lapse (4D) movies and automatically tracked through early cleavage divisions up to ~350 nuclei. A similar analysis of later stages of C. elegans development has been challenging owing to the increased error rates of automated tracking of large numbers of densely packed nuclei. We present Nucleitracker4D, a freely available software solution for tracking nuclei in complex embryos that integrates automated tracking of nuclei in local searches with manual curation. Using these methods, we have been able to track >99% of all nuclei generated in the C. elegans embryo. Our analysis reveals that ventral enclosure of the epidermis is accompanied by complex coordinated migration of the neuronal substrate. We can efficiently track large numbers of migrating nuclei in 4D movies of zebrafish cardiac morphogenesis, suggesting that this approach is generally useful in situations in which the number, packing or dynamics of nuclei present challenges for automated tracking. PMID:23052905

Software engineering and data management for automated payload experiment tool

NASA Technical Reports Server (NTRS)

Maddux, Gary A.; Provancha, Anna; Chattam, David

1994-01-01

The Microgravity Projects Office identified a need to develop a software package that will lead experiment developers through the development planning process, obtain necessary information, establish an electronic data exchange avenue, and allow easier manipulation/reformatting of the collected information. An MS-DOS compatible software package called the Automated Payload Experiment Tool (APET) has been developed and delivered. The objective of this task is to expand on the results of the APET work previously performed by University of Alabama in Huntsville (UAH) and provide versions of the software in a Macintosh and Windows compatible format. Appendix 1 science requirements document (SRD) Users Manual is attached.

DoD Application Store: Enabling C2 Agility?

DTIC Science & Technology

2014-06-01

Framework, will include automated delivery of software patches, web applications, widgets and mobile application packages. The envisioned DoD...Marketplace within the Ozone Widget Framework, will include automated delivery of software patches, web applications, widgets and mobile application...current needs. DoD has started to make inroads within this environment with several Programs of Record (PoR) embracing widgets and other mobile

SSCR Automated Manager (SAM) release 1. 1 reference manual

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

1988-10-01

This manual provides instructions for using the SSCR Automated Manager (SAM) to manage System Software Change Records (SSCRs) online. SSCRs are forms required to document all system software changes for the Martin Marietta Energy Systems, Inc., Central computer systems. SAM, a program developed at Energy Systems, is accessed through IDMS/R (Integrated Database Management System) on an IBM system.

Impact of Automated Software Testing Tools on Reflective Thinking and Student Performance in Introductory Computer Science Programming Classes

ERIC Educational Resources Information Center

Fridge, Evorell; Bagui, Sikha

2016-01-01

The goal of this research was to investigate the effects of automated testing software on levels of student reflection and student performance. This was a self-selecting, between subjects design that examined the performance of students in introductory computer programming classes. Participants were given the option of using the Web-CAT…

Static and Completion Analysis for Planning Knowledge Base Development and Verification

NASA Technical Reports Server (NTRS)

Chien, Steve A.

1996-01-01

A key obstacle hampering fielding of AI planning applications is the considerable expense of developing, verifying, updating, and maintaining the planning knowledge base (KB). Planning systems must be able to compare favorably in terms of software lifecycle costs to other means of automation such as scripts or rule-based expert systems.

Integrating Cost as an Independent Variable Analysis with Evolutionary Acquisition - A Multiattribute Design Evaluation Approach

DTIC Science & Technology

2003-03-01

within the Automated Cost Estimating Integrated Tools ( ACEIT ) software suite (version 5.x). With this capability, one can set cost targets or time...not allow the user to vary more than one decision variable. This limitation of the ACEIT approach thus hinders a holistic view when attempting to

Architectures and Evaluation for Adjustable Control Autonomy for Space-Based Life Support Systems

NASA Technical Reports Server (NTRS)

Malin, Jane T.; Schreckenghost, Debra K.

2001-01-01

In the past five years, a number of automation applications for control of crew life support systems have been developed and evaluated in the Adjustable Autonomy Testbed at NASA's Johnson Space Center. This paper surveys progress on an adjustable autonomous control architecture for situations where software and human operators work together to manage anomalies and other system problems. When problems occur, the level of control autonomy can be adjusted, so that operators and software agents can work together on diagnosis and recovery. In 1997 adjustable autonomy software was developed to manage gas transfer and storage in a closed life support test. Four crewmembers lived and worked in a chamber for 91 days, with both air and water recycling. CO2 was converted to O2 by gas processing systems and wheat crops. With the automation software, significantly fewer hours were spent monitoring operations. System-level validation testing of the software by interactive hybrid simulation revealed problems both in software requirements and implementation. Since that time, we have been developing multi-agent approaches for automation software and human operators, to cooperatively control systems and manage problems. Each new capability has been tested and demonstrated in realistic dynamic anomaly scenarios, using the hybrid simulation tool.

The accuracy of a designed software for automated localization of craniofacial landmarks on CBCT images.

PubMed

Shahidi, Shoaleh; Bahrampour, Ehsan; Soltanimehr, Elham; Zamani, Ali; Oshagh, Morteza; Moattari, Marzieh; Mehdizadeh, Alireza

2014-09-16

Two-dimensional projection radiographs have been traditionally considered the modality of choice for cephalometric analysis. To overcome the shortcomings of two-dimensional images, three-dimensional computed tomography (CT) has been used to evaluate craniofacial structures. However, manual landmark detection depends on medical expertise, and the process is time-consuming. The present study was designed to produce software capable of automated localization of craniofacial landmarks on cone beam (CB) CT images based on image registration and to evaluate its accuracy. The software was designed using MATLAB programming language. The technique was a combination of feature-based (principal axes registration) and voxel similarity-based methods for image registration. A total of 8 CBCT images were selected as our reference images for creating a head atlas. Then, 20 CBCT images were randomly selected as the test images for evaluating the method. Three experts twice located 14 landmarks in all 28 CBCT images during two examinations set 6 weeks apart. The differences in the distances of coordinates of each landmark on each image between manual and automated detection methods were calculated and reported as mean errors. The combined intraclass correlation coefficient for intraobserver reliability was 0.89 and for interobserver reliability 0.87 (95% confidence interval, 0.82 to 0.93). The mean errors of all 14 landmarks were <4 mm. Additionally, 63.57% of landmarks had a mean error of <3 mm compared with manual detection (gold standard method). The accuracy of our approach for automated localization of craniofacial landmarks, which was based on combining feature-based and voxel similarity-based methods for image registration, was acceptable. Nevertheless we recommend repetition of this study using other techniques, such as intensity-based methods.

Application of Novel Software Algorithms to Spectral-Domain Optical Coherence Tomography for Automated Detection of Diabetic Retinopathy.

PubMed

Adhi, Mehreen; Semy, Salim K; Stein, David W; Potter, Daniel M; Kuklinski, Walter S; Sleeper, Harry A; Duker, Jay S; Waheed, Nadia K

2016-05-01

To present novel software algorithms applied to spectral-domain optical coherence tomography (SD-OCT) for automated detection of diabetic retinopathy (DR). Thirty-one diabetic patients (44 eyes) and 18 healthy, nondiabetic controls (20 eyes) who underwent volumetric SD-OCT imaging and fundus photography were retrospectively identified. A retina specialist independently graded DR stage. Trained automated software generated a retinal thickness score signifying macular edema and a cluster score signifying microaneurysms and/or hard exudates for each volumetric SD-OCT. Of 44 diabetic eyes, 38 had DR and six eyes did not have DR. Leave-one-out cross-validation using a linear discriminant at missed detection/false alarm ratio of 3.00 computed software sensitivity and specificity of 92% and 69%, respectively, for DR detection when compared to clinical assessment. Novel software algorithms applied to commercially available SD-OCT can successfully detect DR and may have potential as a viable screening tool for DR in future. [Ophthalmic Surg Lasers Imaging Retina. 2016;47:410-417.]. Copyright 2016, SLACK Incorporated.

The software for automatic creation of the formal grammars used by speech recognition, computer vision, editable text conversion systems, and some new functions

NASA Astrophysics Data System (ADS)

Kardava, Irakli; Tadyszak, Krzysztof; Gulua, Nana; Jurga, Stefan

2017-02-01

For more flexibility of environmental perception by artificial intelligence it is needed to exist the supporting software modules, which will be able to automate the creation of specific language syntax and to make a further analysis for relevant decisions based on semantic functions. According of our proposed approach, of which implementation it is possible to create the couples of formal rules of given sentences (in case of natural languages) or statements (in case of special languages) by helping of computer vision, speech recognition or editable text conversion system for further automatic improvement. In other words, we have developed an approach, by which it can be achieved to significantly improve the training process automation of artificial intelligence, which as a result will give us a higher level of self-developing skills independently from us (from users). At the base of our approach we have developed a software demo version, which includes the algorithm and software code for the entire above mentioned component's implementation (computer vision, speech recognition and editable text conversion system). The program has the ability to work in a multi - stream mode and simultaneously create a syntax based on receiving information from several sources.

Flexible software architecture for user-interface and machine control in laboratory automation.

PubMed

Arutunian, E B; Meldrum, D R; Friedman, N A; Moody, S E

1998-10-01

We describe a modular, layered software architecture for automated laboratory instruments. The design consists of a sophisticated user interface, a machine controller and multiple individual hardware subsystems, each interacting through a client-server architecture built entirely on top of open Internet standards. In our implementation, the user-interface components are built as Java applets that are downloaded from a server integrated into the machine controller. The user-interface client can thereby provide laboratory personnel with a familiar environment for experiment design through a standard World Wide Web browser. Data management and security are seamlessly integrated at the machine-controller layer using QNX, a real-time operating system. This layer also controls hardware subsystems through a second client-server interface. This architecture has proven flexible and relatively easy to implement and allows users to operate laboratory automation instruments remotely through an Internet connection. The software architecture was implemented and demonstrated on the Acapella, an automated fluid-sample-processing system that is under development at the University of Washington.

Driving out errors through tight integration between software and automation.

PubMed

Reifsteck, Mark; Swanson, Thomas; Dallas, Mary

2006-01-01

A clear case has been made for using clinical IT to improve medication safety, particularly bar-code point-of-care medication administration and computerized practitioner order entry (CPOE) with clinical decision support. The equally important role of automation has been overlooked. When the two are tightly integrated, with pharmacy information serving as a hub, the distinctions between software and automation become blurred. A true end-to-end medication management system drives out errors from the dockside to the bedside. Presbyterian Healthcare Services in Albuquerque has been building such a system since 1999, beginning by automating pharmacy operations to support bar-coded medication administration. Encouraged by those results, it then began layering on software to further support clinician workflow and improve communication, culminating with the deployment of CPOE and clinical decision support. This combination, plus a hard-wired culture of safety, has resulted in a dramatically lower mortality and harm rate that could not have been achieved with a partial solution.

Design, Development, and Commissioning of a Substation Automation Laboratory to Enhance Learning

ERIC Educational Resources Information Center

Thomas, M. S.; Kothari, D. P.; Prakash, A.

2011-01-01

Automation of power systems is gaining momentum across the world, and there is a need to expose graduate and undergraduate students to the latest developments in hardware, software, and related protocols for power automation. This paper presents the design, development, and commissioning of an automation lab to facilitate the understanding of…

A test matrix sequencer for research test facility automation

NASA Technical Reports Server (NTRS)

Mccartney, Timothy P.; Emery, Edward F.

1990-01-01

The hardware and software configuration of a Test Matrix Sequencer, a general purpose test matrix profiler that was developed for research test facility automation at the NASA Lewis Research Center, is described. The system provides set points to controllers and contact closures to data systems during the course of a test. The Test Matrix Sequencer consists of a microprocessor controlled system which is operated from a personal computer. The software program, which is the main element of the overall system is interactive and menu driven with pop-up windows and help screens. Analog and digital input/output channels can be controlled from a personal computer using the software program. The Test Matrix Sequencer provides more efficient use of aeronautics test facilities by automating repetitive tasks that were once done manually.

Formal Modeling and Analysis of a Preliminary Small Aircraft Transportation System (SATS)Concept

NASA Technical Reports Server (NTRS)

Carrreno, Victor A.; Gottliebsen, Hanne; Butler, Ricky; Kalvala, Sara

2004-01-01

New concepts for automating air traffic management functions at small non-towered airports raise serious safety issues associated with the software implementations and their underlying key algorithms. The criticality of such software systems necessitates that strong guarantees of the safety be developed for them. In this paper we present a formal method for modeling and verifying such systems using the PVS theorem proving system. The method is demonstrated on a preliminary concept of operation for the Small Aircraft Transportation System (SATS) project at NASA Langley.

Development of program package for investigation and modeling of carbon nanostructures in diamond like carbon films with the help of Raman scattering and infrared absorption spectra line resolving

NASA Astrophysics Data System (ADS)

Hayrapetyan, David B.; Hovhannisyan, Levon; Mantashyan, Paytsar A.

2013-04-01

The analysis of complex spectra is an actual problem for modern science. The work is devoted to the creation of a software package, which analyzes spectrum in the different formats, possesses by dynamic knowledge database and self-study mechanism, performs automated analysis of the spectra compound based on knowledge database by application of certain algorithms. In the software package as searching systems, hyper-spherical random search algorithms, gradient algorithms and genetic searching algorithms were used. The analysis of Raman and IR spectrum of diamond-like carbon (DLC) samples were performed by elaborated program. After processing the data, the program immediately displays all the calculated parameters of DLC.

Automating Embedded Analysis Capabilities and Managing Software Complexity in Multiphysics Simulation, Part II: Application to Partial Differential Equations

DOE PAGES

Pawlowski, Roger P.; Phipps, Eric T.; Salinger, Andrew G.; ...

2012-01-01

A template-based generic programming approach was presented in Part I of this series of papers [Sci. Program. 20 (2012), 197–219] that separates the development effort of programming a physical model from that of computing additional quantities, such as derivatives, needed for embedded analysis algorithms. In this paper, we describe the implementation details for using the template-based generic programming approach for simulation and analysis of partial differential equations (PDEs). We detail several of the hurdles that we have encountered, and some of the software infrastructure developed to overcome them. We end with a demonstration where we present shape optimization and uncertaintymore » quantification results for a 3D PDE application.« less

Discrimination between smiling faces: Human observers vs. automated face analysis.

PubMed

Del Líbano, Mario; Calvo, Manuel G; Fernández-Martín, Andrés; Recio, Guillermo

2018-05-11

This study investigated (a) how prototypical happy faces (with happy eyes and a smile) can be discriminated from blended expressions with a smile but non-happy eyes, depending on type and intensity of the eye expression; and (b) how smile discrimination differs for human perceivers versus automated face analysis, depending on affective valence and morphological facial features. Human observers categorized faces as happy or non-happy, or rated their valence. Automated analysis (FACET software) computed seven expressions (including joy/happiness) and 20 facial action units (AUs). Physical properties (low-level image statistics and visual saliency) of the face stimuli were controlled. Results revealed, first, that some blended expressions (especially, with angry eyes) had lower discrimination thresholds (i.e., they were identified as "non-happy" at lower non-happy eye intensities) than others (especially, with neutral eyes). Second, discrimination sensitivity was better for human perceivers than for automated FACET analysis. As an additional finding, affective valence predicted human discrimination performance, whereas morphological AUs predicted FACET discrimination. FACET can be a valid tool for categorizing prototypical expressions, but is currently more limited than human observers for discrimination of blended expressions. Configural processing facilitates detection of in/congruence(s) across regions, and thus detection of non-genuine smiling faces (due to non-happy eyes). Copyright © 2018 Elsevier B.V. All rights reserved.

Costs to Automate Demand Response - Taxonomy and Results from Field Studies and Programs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Piette, Mary A.; Schetrit, Oren; Kiliccote, Sila

During the past decade, the technology to automate demand response (DR) in buildings and industrial facilities has advanced significantly. Automation allows rapid, repeatable, reliable operation. This study focuses on costs for DR automation in commercial buildings with some discussion on residential buildings and industrial facilities. DR automation technology relies on numerous components, including communication systems, hardware and software gateways, standards-based messaging protocols, controls and integration platforms, and measurement and telemetry systems. This report compares cost data from several DR automation programs and pilot projects, evaluates trends in the cost per unit of DR and kilowatts (kW) available from automated systems,more » and applies a standard naming convention and classification or taxonomy for system elements. Median costs for the 56 installed automated DR systems studied here are about $200/kW. The deviation around this median is large with costs in some cases being an order of magnitude great or less than the median. This wide range is a result of variations in system age, size of load reduction, sophistication, and type of equipment included in cost analysis. The costs to automate fast DR systems for ancillary services are not fully analyzed in this report because additional research is needed to determine the total cost to install, operate, and maintain these systems. However, recent research suggests that they could be developed at costs similar to those of existing hot-summer DR automation systems. This report considers installation and configuration costs and does include the costs of owning and operating DR automation systems. Future analysis of the latter costs should include the costs to the building or facility manager costs as well as utility or third party program manager cost.« less

Space shuttle main engine anomaly data and inductive knowledge based systems: Automated corporate expertise

NASA Technical Reports Server (NTRS)

Modesitt, Kenneth L.

1987-01-01

Progress is reported on the development of SCOTTY, an expert knowledge-based system to automate the analysis procedure following test firings of the Space Shuttle Main Engine (SSME). The integration of a large-scale relational data base system, a computer graphics interface for experts and end-user engineers, potential extension of the system to flight engines, application of the system for training of newly-hired engineers, technology transfer to other engines, and the essential qualities of good software engineering practices for building expert knowledge-based systems are among the topics discussed.

Issues in advanced automation for manipulator control

NASA Technical Reports Server (NTRS)

Bejczy, A. K.

1976-01-01

This paper provides a brief description and analysis of the main issues in advanced autonomous control of manipulators as seen from a system point of view. The nature of manipulation is analyzed at some depth. A general multilevel structure is outlined for manipulator control organization which includes the human operator at the top level of the control structure. Different approaches to the development of advanced automation of mechanical arms are summarized. Recent work in the JPL teleoperator project is described, including control system, force/torque sensor, and control software development. Some results from control experiments are summarized.

A software platform for the analysis of dermatology images

NASA Astrophysics Data System (ADS)

Vlassi, Maria; Mavraganis, Vlasios; Asvestas, Panteleimon

2017-11-01

The purpose of this paper is to present a software platform developed in Python programming environment that can be used for the processing and analysis of dermatology images. The platform provides the capability for reading a file that contains a dermatology image. The platform supports image formats such as Windows bitmaps, JPEG, JPEG2000, portable network graphics, TIFF. Furthermore, it provides suitable tools for selecting, either manually or automatically, a region of interest (ROI) on the image. The automated selection of a ROI includes filtering for smoothing the image and thresholding. The proposed software platform has a friendly and clear graphical user interface and could be a useful second-opinion tool to a dermatologist. Furthermore, it could be used to classify images including from other anatomical parts such as breast or lung, after proper re-training of the classification algorithms.

Automated Retroillumination Photography Analysis for Objective Assessment of Fuchs Corneal Dystrophy.

PubMed

Eghrari, Allen O; Mumtaz, Aisha A; Garrett, Brian; Rezaei, Mahsa; Akhavan, Mina S; Riazuddin, S Amer; Gottsch, John D

2017-01-01

Retroillumination photography analysis is an objective tool for the assessment of the number and distribution of guttae in eyes affected with Fuchs corneal dystrophy (FCD). Current protocols include manual processing of images; here, we assess validity and interrater reliability of automated analysis across various levels of FCD severity. Retroillumination photographs of 97 FCD-affected corneas were acquired, and total counts of guttae were previously summated manually. For each cornea, a single image was loaded into ImageJ software. We reduced color variability and subtracted background noise. Reflection of light from each gutta was identified as a local area of maximum intensity and counted automatically. Noise tolerance level was titrated for each cornea by examining a small region of each image with automated overlay to ensure appropriate coverage of individual guttae. We tested interrater reliability of automated counts of guttae across a spectrum of clinical and educational experience. A set of 97 retroillumination photographs was analyzed. Clinical severity as measured by a modified Krachmer scale ranged from a severity level of 1 to 5 in the set of analyzed corneas. Automated counts by an ophthalmologist correlated strongly with Krachmer grading (R = 0.79) and manual counts (R = 0.88). Intraclass correlation coefficients demonstrated strong correlation at 0.924 (95% CI, 0.870-0.958) among cases analyzed by 3 students, and 0.869 (95% CI, 0.797-0.918) among cases for which images were analyzed by an ophthalmologist and 2 students. Automated retroillumination photography analysis allows for grading of FCD severity with high resolution across a spectrum of disease severity.

Quantitative analyses for elucidating mechanisms of cell fate commitment in the mouse blastocyst

NASA Astrophysics Data System (ADS)

Saiz, Néstor; Kang, Minjung; Puliafito, Alberto; Schrode, Nadine; Xenopoulos, Panagiotis; Lou, Xinghua; Di Talia, Stefano; Hadjantonakis, Anna-Katerina

2015-03-01

In recent years we have witnessed a shift from qualitative image analysis towards higher resolution, quantitative analyses of imaging data in developmental biology. This shift has been fueled by technological advances in both imaging and analysis software. We have recently developed a tool for accurate, semi-automated nuclear segmentation of imaging data from early mouse embryos and embryonic stem cells. We have applied this software to the study of the first lineage decisions that take place during mouse development and established analysis pipelines for both static and time-lapse imaging experiments. In this paper we summarize the conclusions from these studies to illustrate how quantitative, single-cell level analysis of imaging data can unveil biological processes that cannot be revealed by traditional qualitative studies.

Subunit mass analysis for monitoring antibody oxidation.

PubMed

Sokolowska, Izabela; Mo, Jingjie; Dong, Jia; Lewis, Michael J; Hu, Ping

2017-04-01

Methionine oxidation is a common posttranslational modification (PTM) of monoclonal antibodies (mAbs). Oxidation can reduce the in-vivo half-life, efficacy and stability of the product. Peptide mapping is commonly used to monitor the levels of oxidation, but this is a relatively time-consuming method. A high-throughput, automated subunit mass analysis method was developed to monitor antibody methionine oxidation. In this method, samples were treated with IdeS, EndoS and dithiothreitol to generate three individual IgG subunits (light chain, Fd' and single chain Fc). These subunits were analyzed by reversed phase-ultra performance liquid chromatography coupled with an online quadrupole time-of-flight mass spectrometer and the levels of oxidation on each subunit were quantitated based on the deconvoluted mass spectra using the UNIFI software. The oxidation results obtained by subunit mass analysis correlated well with the results obtained by peptide mapping. Method qualification demonstrated that this subunit method had excellent repeatability and intermediate precision. In addition, UNIFI software used in this application allows automated data acquisition and processing, which makes this method suitable for high-throughput process monitoring and product characterization. Finally, subunit mass analysis revealed the different patterns of Fc methionine oxidation induced by chemical and photo stress, which makes it attractive for investigating the root cause of oxidation.

Automatic Detection of Previously-Unseen Application States for Deployment Environment Testing and Analysis

PubMed Central

Murphy, Christian; Vaughan, Moses; Ilahi, Waseem; Kaiser, Gail

2010-01-01

For large, complex software systems, it is typically impossible in terms of time and cost to reliably test the application in all possible execution states and configurations before releasing it into production. One proposed way of addressing this problem has been to continue testing and analysis of the application in the field, after it has been deployed. A practical limitation of many such automated approaches is the potentially high performance overhead incurred by the necessary instrumentation. However, it may be possible to reduce this overhead by selecting test cases and performing analysis only in previously-unseen application states, thus reducing the number of redundant tests and analyses that are run. Solutions for fault detection, model checking, security testing, and fault localization in deployed software may all benefit from a technique that ignores application states that have already been tested or explored. In this paper, we present a solution that ensures that deployment environment tests are only executed in states that the application has not previously encountered. In addition to discussing our implementation, we present the results of an empirical study that demonstrates its effectiveness, and explain how the new approach can be generalized to assist other automated testing and analysis techniques intended for the deployment environment. PMID:21197140

Development of image analysis software for quantification of viable cells in microchips.

PubMed

Georg, Maximilian; Fernández-Cabada, Tamara; Bourguignon, Natalia; Karp, Paola; Peñaherrera, Ana B; Helguera, Gustavo; Lerner, Betiana; Pérez, Maximiliano S; Mertelsmann, Roland

2018-01-01

Over the past few years, image analysis has emerged as a powerful tool for analyzing various cell biology parameters in an unprecedented and highly specific manner. The amount of data that is generated requires automated methods for the processing and analysis of all the resulting information. The software available so far are suitable for the processing of fluorescence and phase contrast images, but often do not provide good results from transmission light microscopy images, due to the intrinsic variation of the acquisition of images technique itself (adjustment of brightness / contrast, for instance) and the variability between image acquisition introduced by operators / equipment. In this contribution, it has been presented an image processing software, Python based image analysis for cell growth (PIACG), that is able to calculate the total area of the well occupied by cells with fusiform and rounded morphology in response to different concentrations of fetal bovine serum in microfluidic chips, from microscopy images in transmission light, in a highly efficient way.

Advanced Cell Classifier: User-Friendly Machine-Learning-Based Software for Discovering Phenotypes in High-Content Imaging Data.

PubMed

Piccinini, Filippo; Balassa, Tamas; Szkalisity, Abel; Molnar, Csaba; Paavolainen, Lassi; Kujala, Kaisa; Buzas, Krisztina; Sarazova, Marie; Pietiainen, Vilja; Kutay, Ulrike; Smith, Kevin; Horvath, Peter

2017-06-28

High-content, imaging-based screens now routinely generate data on a scale that precludes manual verification and interrogation. Software applying machine learning has become an essential tool to automate analysis, but these methods require annotated examples to learn from. Efficiently exploring large datasets to find relevant examples remains a challenging bottleneck. Here, we present Advanced Cell Classifier (ACC), a graphical software package for phenotypic analysis that addresses these difficulties. ACC applies machine-learning and image-analysis methods to high-content data generated by large-scale, cell-based experiments. It features methods to mine microscopic image data, discover new phenotypes, and improve recognition performance. We demonstrate that these features substantially expedite the training process, successfully uncover rare phenotypes, and improve the accuracy of the analysis. ACC is extensively documented, designed to be user-friendly for researchers without machine-learning expertise, and distributed as a free open-source tool at www.cellclassifier.org. Copyright © 2017 Elsevier Inc. All rights reserved.

NASA Tech Briefs, September 2006

NASA Technical Reports Server (NTRS)

2006-01-01

Topics covered include: Improving Thermomechanical Properties of SiC/SiC Composites; Aerogel/Particle Composites for Thermoelectric Devices; Patches for Repairing Ceramics and Ceramic- Matrix Composites; Lower-Conductivity Ceramic Materials for Thermal-Barrier Coatings; An Alternative for Emergency Preemption of Traffic Lights; Vehicle Transponder for Preemption of Traffic Lights; Automated Announcements of Approaching Emergency Vehicles; Intersection Monitor for Traffic-Light-Preemption System; Full-Duplex Digital Communication on a Single Laser Beam; Stabilizing Microwave Frequency of a Photonic Oscillator; Microwave Oscillators Based on Nonlinear WGM Resonators; Pointing Reference Scheme for Free-Space Optical Communications Systems; High-Level Performance Modeling of SAR Systems; Spectral Analysis Tool 6.2 for Windows; Multi-Platform Avionics Simulator; Silicon-Based Optical Modulator with Ferroelectric Layer; Multiplexing Transducers Based on Tunnel-Diode Oscillators; Scheduling with Automated Resolution of Conflicts; Symbolic Constraint Maintenance Grid; Discerning Trends in Performance Across Multiple Events; Magnetic Field Solver; Computing for Aiming a Spaceborne Bistatic- Radar Transmitter; 4-Vinyl-1,3-Dioxolane-2-One as an Additive for Li-Ion Cells; Probabilistic Prediction of Lifetimes of Ceramic Parts; STRANAL-PMC Version 2.0; Micromechanics and Piezo Enhancements of HyperSizer; Single-Phase Rare-Earth Oxide/Aluminum Oxide Glasses; Tilt/Tip/Piston Manipulator with Base-Mounted Actuators; Measurement of Model Noise in a Hard-Wall Wind Tunnel; Loci-STREAM Version 0.9; The Synergistic Engineering Environment; Reconfigurable Software for Controlling Formation Flying; More About the Tetrahedral Unstructured Software System; Computing Flows Using Chimera and Unstructured Grids; Avoiding Obstructions in Aiming a High-Gain Antenna; Analyzing Aeroelastic Stability of a Tilt-Rotor Aircraft; Tracking Positions and Attitudes of Mars Rovers; Stochastic Evolutionary Algorithms for Planning Robot Paths; Compressible Flow Toolbox; Rapid Aeroelastic Analysis of Blade Flutter in Turbomachines; General Flow-Solver Code for Turbomachinery Applications; Code for Multiblock CFD and Heat-Transfer Computations; Rotating-Pump Design Code; Covering a Crucible with Metal Containing Channels; Repairing Fractured Bones by Use of Bioabsorbable Composites; Kalman Filter for Calibrating a Telescope Focal Plane; Electronic Absolute Cartesian Autocollimator; Fiber-Optic Gratings for Lidar Measurements of Water Vapor; Simulating Responses of Gravitational-Wave Instrumentation; SOFTC: A Software Correlator for VLBI; Progress in Computational Simulation of Earthquakes; Database of Properties of Meteors; Computing Spacecraft Solar-Cell Damage by Charged Particles; Thermal Model of a Current-Carrying Wire in a Vacuum; Program for Analyzing Flows in a Complex Network; Program Predicts Performance of Optical Parametric Oscillators; Processing TES Level-1B Data; Automated Camera Calibration; Tracking the Martian CO2 Polar Ice Caps in Infrared Images; Processing TES Level-2 Data; SmaggIce Version 1.8; Solving the Swath Segment Selection Problem; The Spatial Standard Observer; Less-Complex Method of Classifying MPSK; Improvement in Recursive Hierarchical Segmentation of Data; Using Heaps in Recursive Hierarchical Segmentation of Data; Tool for Statistical Analysis and Display of Landing Sites; Automated Assignment of Proposals to Reviewers; Array-Pattern-Match Compiler for Opportunistic Data Analysis; Pre-Processor for Compression of Multispectral Image Data; Compressing Image Data While Limiting the Effects of Data Losses; Flight Operations Analysis Tool; Improvement in Visual Target Tracking for a Mobile Robot; Software for Simulating Air Traffic; Automated Vectorization of Decision-Based Algorithms; Grayscale Optical Correlator Workbench; "One-Stop Shopping" for Ocean Remote-Sensing and Model Data; State Analysis Database Tool; Generating CAHV and CAHVOmages with Shadows in ROAMS; Improving UDP/IP Transmission Without Increasing Congestion; FORTRAN Versions of Reformulated HFGMC Codes; Program for Editing Spacecraft Command Sequences; Flight-Tested Prototype of BEAM Software; Mission Scenario Development Workbench; Marsviewer; Tool for Analysis and Reduction of Scientific Data; ASPEN Version 3.0; Secure Display of Space-Exploration Images; Digital Front End for Wide-Band VLBI Science Receiver; Multifunctional Tanks for Spacecraft; Lightweight, Segmented, Mostly Silicon Telescope Mirror; Assistant for Analyzing Tropical-Rain-Mapping Radar Data; and Anion-Intercalating Cathodes for High-Energy- Density Cells.

Laboratory automation: trajectory, technology, and tactics.

PubMed

Markin, R S; Whalen, S A

2000-05-01

Laboratory automation is in its infancy, following a path parallel to the development of laboratory information systems in the late 1970s and early 1980s. Changes on the horizon in healthcare and clinical laboratory service that affect the delivery of laboratory results include the increasing age of the population in North America, the implementation of the Balanced Budget Act (1997), and the creation of disease management companies. Major technology drivers include outcomes optimization and phenotypically targeted drugs. Constant cost pressures in the clinical laboratory have forced diagnostic manufacturers into less than optimal profitability states. Laboratory automation can be a tool for the improvement of laboratory services and may decrease costs. The key to improvement of laboratory services is implementation of the correct automation technology. The design of this technology should be driven by required functionality. Automation design issues should be centered on the understanding of the laboratory and its relationship to healthcare delivery and the business and operational processes in the clinical laboratory. Automation design philosophy has evolved from a hardware-based approach to a software-based approach. Process control software to support repeat testing, reflex testing, and transportation management, and overall computer-integrated manufacturing approaches to laboratory automation implementation are rapidly expanding areas. It is clear that hardware and software are functionally interdependent and that the interface between the laboratory automation system and the laboratory information system is a key component. The cost-effectiveness of automation solutions suggested by vendors, however, has been difficult to evaluate because the number of automation installations are few and the precision with which operational data have been collected to determine payback is suboptimal. The trend in automation has moved from total laboratory automation to a modular approach, from a hardware-driven system to process control, from a one-of-a-kind novelty toward a standardized product, and from an in vitro diagnostics novelty to a marketing tool. Multiple vendors are present in the marketplace, many of whom are in vitro diagnostics manufacturers providing an automation solution coupled with their instruments, whereas others are focused automation companies. Automation technology continues to advance, acceptance continues to climb, and payback and cost justification methods are developing.

Flight Operations Analysis Tool

NASA Technical Reports Server (NTRS)

Easter, Robert; Herrell, Linda; Pomphrey, Richard; Chase, James; Wertz Chen, Julie; Smith, Jeffrey; Carter, Rebecca

2006-01-01

Flight Operations Analysis Tool (FLOAT) is a computer program that partly automates the process of assessing the benefits of planning spacecraft missions to incorporate various combinations of launch vehicles and payloads. Designed primarily for use by an experienced systems engineer, FLOAT makes it possible to perform a preliminary analysis of trade-offs and costs of a proposed mission in days, whereas previously, such an analysis typically lasted months. FLOAT surveys a variety of prior missions by querying data from authoritative NASA sources pertaining to 20 to 30 mission and interface parameters that define space missions. FLOAT provides automated, flexible means for comparing the parameters to determine compatibility or the lack thereof among payloads, spacecraft, and launch vehicles, and for displaying the results of such comparisons. Sparseness, typical of the data available for analysis, does not confound this software. FLOAT effects an iterative process that identifies modifications of parameters that could render compatible an otherwise incompatible mission set.

GSOSTATS Database: USAF Synchronous Satellite Catalog Data Conversion Software. User's Guide and Software Maintenance Manual, Version 2.1

NASA Technical Reports Server (NTRS)

Mallasch, Paul G.; Babic, Slavoljub

1994-01-01

The United States Air Force (USAF) provides NASA Lewis Research Center with monthly reports containing the Synchronous Satellite Catalog and the associated Two Line Mean Element Sets. The USAF Synchronous Satellite Catalog supplies satellite orbital parameters collected by an automated monitoring system and provided to Lewis Research Center as text files on magnetic tape. Software was developed to facilitate automated formatting, data normalization, cross-referencing, and error correction of Synchronous Satellite Catalog files before loading into the NASA Geosynchronous Satellite Orbital Statistics Database System (GSOSTATS). This document contains the User's Guide and Software Maintenance Manual with information necessary for installation, initialization, start-up, operation, error recovery, and termination of the software application. It also contains implementation details, modification aids, and software source code adaptations for use in future revisions.

Automated respiratory cycles selection is highly specific and improves respiratory mechanics analysis.

PubMed

Rigo, Vincent; Graas, Estelle; Rigo, Jacques

2012-07-01

Selected optimal respiratory cycles should allow calculation of respiratory mechanic parameters focusing on patient-ventilator interaction. New computer software automatically selecting optimal breaths and respiratory mechanics derived from those cycles are evaluated. Retrospective study. University level III neonatal intensive care unit. Ten mins synchronized intermittent mandatory ventilation and assist/control ventilation recordings from ten newborns. The ventilator provided respiratory mechanic data (ventilator respiratory cycles) every 10 secs. Pressure, flow, and volume waves and pressure-volume, pressure-flow, and volume-flow loops were reconstructed from continuous pressure-volume recordings. Visual assessment determined assisted leak-free optimal respiratory cycles (selected respiratory cycles). New software graded the quality of cycles (automated respiratory cycles). Respiratory mechanic values were derived from both sets of optimal cycles. We evaluated quality selection and compared mean values and their variability according to ventilatory mode and respiratory mechanic provenance. To assess discriminating power, all 45 "t" values obtained from interpatient comparisons were compared for each respiratory mechanic parameter. A total of 11,724 breaths are evaluated. Automated respiratory cycle/selected respiratory cycle selections agreement is high: 88% of maximal κ with linear weighting. Specificity and positive predictive values are 0.98 and 0.96, respectively. Averaged values are similar between automated respiratory cycle and ventilator respiratory cycle. C20/C alone is markedly decreased in automated respiratory cycle (1.27 ± 0.37 vs. 1.81 ± 0.67). Tidal volume apparent similarity disappears in assist/control: automated respiratory cycle tidal volume (4.8 ± 1.0 mL/kg) is significantly lower than for ventilator respiratory cycle (5.6 ± 1.8 mL/kg). Coefficients of variation decrease for all automated respiratory cycle parameters in all infants. "t" values from ventilator respiratory cycle data are two to three times higher than ventilator respiratory cycles. Automated selection is highly specific. Automated respiratory cycle reflects most the interaction of both ventilator and patient. Improving discriminating power of ventilator monitoring will likely help in assessing disease status and following trends. Averaged parameters derived from automated respiratory cycles are more precise and could be displayed by ventilators to improve real-time fine tuning of ventilator settings.

Evaluation of automated image analysis software for the detection of diabetic retinopathy to reduce the ophthalmologists' workload.

PubMed

Soto-Pedre, Enrique; Navea, Amparo; Millan, Saray; Hernaez-Ortega, Maria C; Morales, Jesús; Desco, Maria C; Pérez, Pablo

2015-02-01

To assess the safety and workload reduction of an automated 'disease/no disease' grading system for diabetic retinopathy (DR) within a systematic screening programme. Single 45° macular field image per eye was obtained from consecutive patients attending a regional primary care based DR screening programme in Valencia (Spain). The sensitivity and specificity of automated system operating as 'one or more than one microaneurysm detection for disease presence' grader were determined relative to a manual grading as gold standard. Data on age, gender and diabetes mellitus were also recorded. A total of 5278 patients with diabetes were screened. The median age and duration of diabetes was 69 years and 6.9 years, respectively. Estimated prevalence of DR was 15.6%. The software classified 43.9% of the patients as having no DR and 26.1% as having ungradable images. Detection of DR was achieved with 94.5% sensitivity (95% CI 92.6- 96.5) and 68.8% specificity (95%CI 67.2-70.4). The overall accuracy of the automated system was 72.5% (95%CI 71.1-73.9). The present retinal image processing algorithm that can act as prefilter to flag out images with pathological lesions can be implemented in practice. Our results suggest that it could be considered when implementing DR screening programmes. © 2014 Acta Ophthalmologica Scandinavica Foundation. Published by John Wiley & Sons Ltd.

An interactive dynamic analysis and decision support software for MR mammography.

PubMed

Ertaş, Gökhan; Gülçür, H Ozcan; Tunaci, Mehtap

2008-06-01

A fully automated software is introduced to facilitate MR mammography (MRM) examinations and overcome subjectiveness in diagnosis using normalized maximum intensity-time ratio (nMITR) maps. These maps inherently suppress enhancements due to normal parenchyma and blood vessels that surround lesions and have natural tolerance to small field inhomogeneities and motion artifacts. The classifier embedded within the software is trained with normalized complexity and maximum nMITR of 22 lesions and tested with the features of remaining 22 lesions. Achieved diagnostic performances are 92% sensitivity, 90% specificity, 91% accuracy, 92% positive predictive value and 90% negative predictive value. DynaMammoAnalyst shortens evaluation time considerably and reduces inter and intra-observer variability by providing decision support.

Paramedir: A Tool for Programmable Performance Analysis

NASA Technical Reports Server (NTRS)

Jost, Gabriele; Labarta, Jesus; Gimenez, Judit

2004-01-01

Performance analysis of parallel scientific applications is time consuming and requires great expertise in areas such as programming paradigms, system software, and computer hardware architectures. In this paper we describe a tool that facilitates the programmability of performance metric calculations thereby allowing the automation of the analysis and reducing the application development time. We demonstrate how the system can be used to capture knowledge and intuition acquired by advanced parallel programmers in order to be transferred to novice users.

Automated Scheduling Via Artificial Intelligence

NASA Technical Reports Server (NTRS)

Biefeld, Eric W.; Cooper, Lynne P.

1991-01-01

Artificial-intelligence software that automates scheduling developed in Operations Mission Planner (OMP) research project. Software used in both generation of new schedules and modification of existing schedules in view of changes in tasks and/or available resources. Approach based on iterative refinement. Although project focused upon scheduling of operations of scientific instruments and other equipment aboard spacecraft, also applicable to such terrestrial problems as scheduling production in factory.

The development of a strategy for the implementation of automation in a bioanalytical laboratory.

PubMed

Mole, D; Mason, R J; McDowall, R D

1993-03-01

Laboratory automation is equipment, instrumentation, software and techniques that are classified into four groups: instrument automation; communications; data to information conversion; and information management. This new definition is necessary to understand the role that automation can play in achieving the aims and objectives of a laboratory within its organization. To undertake automation projects effectively, a laboratory automation strategy is outlined which requires an intimate knowledge of an organization and the target environment to implement individual automation projects.

Validation of automated white matter hyperintensity segmentation.

PubMed

Smart, Sean D; Firbank, Michael J; O'Brien, John T

2011-01-01

Introduction. White matter hyperintensities (WMHs) are a common finding on MRI scans of older people and are associated with vascular disease. We compared 3 methods for automatically segmenting WMHs from MRI scans. Method. An operator manually segmented WMHs on MRI images from a 3T scanner. The scans were also segmented in a fully automated fashion by three different programmes. The voxel overlap between manual and automated segmentation was compared. Results. Between observer overlap ratio was 63%. Using our previously described in-house software, we had overlap of 62.2%. We investigated the use of a modified version of SPM segmentation; however, this was not successful, with only 14% overlap. Discussion. Using our previously reported software, we demonstrated good segmentation of WMHs in a fully automated fashion.

FoodChain-Lab: A Trace-Back and Trace-Forward Tool Developed and Applied during Food-Borne Disease Outbreak Investigations in Germany and Europe.

PubMed

Weiser, Armin A; Thöns, Christian; Filter, Matthias; Falenski, Alexander; Appel, Bernd; Käsbohrer, Annemarie

2016-01-01

FoodChain-Lab is modular open-source software for trace-back and trace-forward analysis in food-borne disease outbreak investigations. Development of FoodChain-Lab has been driven by a need for appropriate software in several food-related outbreaks in Germany since 2011. The software allows integrated data management, data linkage, enrichment and visualization as well as interactive supply chain analyses. Identification of possible outbreak sources or vehicles is facilitated by calculation of tracing scores for food-handling stations (companies or persons) and food products under investigation. The software also supports consideration of station-specific cross-contamination, analysis of geographical relationships, and topological clustering of the tracing network structure. FoodChain-Lab has been applied successfully in previous outbreak investigations, for example during the 2011 EHEC outbreak and the 2013/14 European hepatitis A outbreak. The software is most useful in complex, multi-area outbreak investigations where epidemiological evidence may be insufficient to discriminate between multiple implicated food products. The automated analysis and visualization components would be of greater value if trading information on food ingredients and compound products was more easily available.

FoodChain-Lab: A Trace-Back and Trace-Forward Tool Developed and Applied during Food-Borne Disease Outbreak Investigations in Germany and Europe

PubMed Central

Filter, Matthias; Falenski, Alexander; Appel, Bernd; Käsbohrer, Annemarie

2016-01-01

FoodChain-Lab is modular open-source software for trace-back and trace-forward analysis in food-borne disease outbreak investigations. Development of FoodChain-Lab has been driven by a need for appropriate software in several food-related outbreaks in Germany since 2011. The software allows integrated data management, data linkage, enrichment and visualization as well as interactive supply chain analyses. Identification of possible outbreak sources or vehicles is facilitated by calculation of tracing scores for food-handling stations (companies or persons) and food products under investigation. The software also supports consideration of station-specific cross-contamination, analysis of geographical relationships, and topological clustering of the tracing network structure. FoodChain-Lab has been applied successfully in previous outbreak investigations, for example during the 2011 EHEC outbreak and the 2013/14 European hepatitis A outbreak. The software is most useful in complex, multi-area outbreak investigations where epidemiological evidence may be insufficient to discriminate between multiple implicated food products. The automated analysis and visualization components would be of greater value if trading information on food ingredients and compound products was more easily available. PMID:26985673

Quantification of Pulmonary Fibrosis in a Bleomycin Mouse Model Using Automated Histological Image Analysis.

PubMed

Gilhodes, Jean-Claude; Julé, Yvon; Kreuz, Sebastian; Stierstorfer, Birgit; Stiller, Detlef; Wollin, Lutz

2017-01-01

Current literature on pulmonary fibrosis induced in animal models highlights the need of an accurate, reliable and reproducible histological quantitative analysis. One of the major limits of histological scoring concerns the fact that it is observer-dependent and consequently subject to variability, which may preclude comparative studies between different laboratories. To achieve a reliable and observer-independent quantification of lung fibrosis we developed an automated software histological image analysis performed from digital image of entire lung sections. This automated analysis was compared to standard evaluation methods with regard to its validation as an end-point measure of fibrosis. Lung fibrosis was induced in mice by intratracheal administration of bleomycin (BLM) at 0.25, 0.5, 0.75 and 1 mg/kg. A detailed characterization of BLM-induced fibrosis was performed 14 days after BLM administration using lung function testing, micro-computed tomography and Ashcroft scoring analysis. Quantification of fibrosis by automated analysis was assessed based on pulmonary tissue density measured from thousands of micro-tiles processed from digital images of entire lung sections. Prior to analysis, large bronchi and vessels were manually excluded from the original images. Measurement of fibrosis has been expressed by two indexes: the mean pulmonary tissue density and the high pulmonary tissue density frequency. We showed that tissue density indexes gave access to a very accurate and reliable quantification of morphological changes induced by BLM even for the lowest concentration used (0.25 mg/kg). A reconstructed 2D-image of the entire lung section at high resolution (3.6 μm/pixel) has been performed from tissue density values allowing the visualization of their distribution throughout fibrotic and non-fibrotic regions. A significant correlation (p<0.0001) was found between automated analysis and the above standard evaluation methods. This correlation establishes automated analysis as a novel end-point measure of BLM-induced lung fibrosis in mice, which will be very valuable for future preclinical drug explorations.

Quantification of Pulmonary Fibrosis in a Bleomycin Mouse Model Using Automated Histological Image Analysis

PubMed Central

Gilhodes, Jean-Claude; Kreuz, Sebastian; Stierstorfer, Birgit; Stiller, Detlef; Wollin, Lutz

2017-01-01

Current literature on pulmonary fibrosis induced in animal models highlights the need of an accurate, reliable and reproducible histological quantitative analysis. One of the major limits of histological scoring concerns the fact that it is observer-dependent and consequently subject to variability, which may preclude comparative studies between different laboratories. To achieve a reliable and observer-independent quantification of lung fibrosis we developed an automated software histological image analysis performed from digital image of entire lung sections. This automated analysis was compared to standard evaluation methods with regard to its validation as an end-point measure of fibrosis. Lung fibrosis was induced in mice by intratracheal administration of bleomycin (BLM) at 0.25, 0.5, 0.75 and 1 mg/kg. A detailed characterization of BLM-induced fibrosis was performed 14 days after BLM administration using lung function testing, micro-computed tomography and Ashcroft scoring analysis. Quantification of fibrosis by automated analysis was assessed based on pulmonary tissue density measured from thousands of micro-tiles processed from digital images of entire lung sections. Prior to analysis, large bronchi and vessels were manually excluded from the original images. Measurement of fibrosis has been expressed by two indexes: the mean pulmonary tissue density and the high pulmonary tissue density frequency. We showed that tissue density indexes gave access to a very accurate and reliable quantification of morphological changes induced by BLM even for the lowest concentration used (0.25 mg/kg). A reconstructed 2D-image of the entire lung section at high resolution (3.6 μm/pixel) has been performed from tissue density values allowing the visualization of their distribution throughout fibrotic and non-fibrotic regions. A significant correlation (p<0.0001) was found between automated analysis and the above standard evaluation methods. This correlation establishes automated analysis as a novel end-point measure of BLM-induced lung fibrosis in mice, which will be very valuable for future preclinical drug explorations. PMID:28107543

NMRNet: A deep learning approach to automated peak picking of protein NMR spectra.

PubMed

Klukowski, Piotr; Augoff, Michal; Zieba, Maciej; Drwal, Maciej; Gonczarek, Adam; Walczak, Michal J

2018-03-14

Automated selection of signals in protein NMR spectra, known as peak picking, has been studied for over 20 years, nevertheless existing peak picking methods are still largely deficient. Accurate and precise automated peak picking would accelerate the structure calculation, and analysis of dynamics and interactions of macromolecules. Recent advancement in handling big data, together with an outburst of machine learning techniques, offer an opportunity to tackle the peak picking problem substantially faster than manual picking and on par with human accuracy. In particular, deep learning has proven to systematically achieve human-level performance in various recognition tasks, and thus emerges as an ideal tool to address automated identification of NMR signals. We have applied a convolutional neural network for visual analysis of multidimensional NMR spectra. A comprehensive test on 31 manually-annotated spectra has demonstrated top-tier average precision (AP) of 0.9596, 0.9058 and 0.8271 for backbone, side-chain and NOESY spectra, respectively. Furthermore, a combination of extracted peak lists with automated assignment routine, FLYA, outperformed other methods, including the manual one, and led to correct resonance assignment at the levels of 90.40%, 89.90% and 90.20% for three benchmark proteins. The proposed model is a part of a Dumpling software (platform for protein NMR data analysis), and is available at https://dumpling.bio/. michaljerzywalczak@gmail.compiotr.klukowski@pwr.edu.pl. Supplementary data are available at Bioinformatics online.

Cardiac imaging: working towards fully-automated machine analysis & interpretation

PubMed Central

Slomka, Piotr J; Dey, Damini; Sitek, Arkadiusz; Motwani, Manish; Berman, Daniel S; Germano, Guido

2017-01-01

Introduction Non-invasive imaging plays a critical role in managing patients with cardiovascular disease. Although subjective visual interpretation remains the clinical mainstay, quantitative analysis facilitates objective, evidence-based management, and advances in clinical research. This has driven developments in computing and software tools aimed at achieving fully automated image processing and quantitative analysis. In parallel, machine learning techniques have been used to rapidly integrate large amounts of clinical and quantitative imaging data to provide highly personalized individual patient-based conclusions. Areas covered This review summarizes recent advances in automated quantitative imaging in cardiology and describes the latest techniques which incorporate machine learning principles. The review focuses on the cardiac imaging techniques which are in wide clinical use. It also discusses key issues and obstacles for these tools to become utilized in mainstream clinical practice. Expert commentary Fully-automated processing and high-level computer interpretation of cardiac imaging are becoming a reality. Application of machine learning to the vast amounts of quantitative data generated per scan and integration with clinical data also facilitates a move to more patient-specific interpretation. These developments are unlikely to replace interpreting physicians but will provide them with highly accurate tools to detect disease, risk-stratify, and optimize patient-specific treatment. However, with each technological advance, we move further from human dependence and closer to fully-automated machine interpretation. PMID:28277804

ACQ4: an open-source software platform for data acquisition and analysis in neurophysiology research.

PubMed

Campagnola, Luke; Kratz, Megan B; Manis, Paul B

2014-01-01

The complexity of modern neurophysiology experiments requires specialized software to coordinate multiple acquisition devices and analyze the collected data. We have developed ACQ4, an open-source software platform for performing data acquisition and analysis in experimental neurophysiology. This software integrates the tasks of acquiring, managing, and analyzing experimental data. ACQ4 has been used primarily for standard patch-clamp electrophysiology, laser scanning photostimulation, multiphoton microscopy, intrinsic imaging, and calcium imaging. The system is highly modular, which facilitates the addition of new devices and functionality. The modules included with ACQ4 provide for rapid construction of acquisition protocols, live video display, and customizable analysis tools. Position-aware data collection allows automated construction of image mosaics and registration of images with 3-dimensional anatomical atlases. ACQ4 uses free and open-source tools including Python, NumPy/SciPy for numerical computation, PyQt for the user interface, and PyQtGraph for scientific graphics. Supported hardware includes cameras, patch clamp amplifiers, scanning mirrors, lasers, shutters, Pockels cells, motorized stages, and more. ACQ4 is available for download at http://www.acq4.org.

Automated software development workstation

NASA Technical Reports Server (NTRS)

Prouty, Dale A.; Klahr, Philip

1988-01-01

A workstation is being developed that provides a computational environment for all NASA engineers across application boundaries, which automates reuse of existing NASA software and designs, and efficiently and effectively allows new programs and/or designs to be developed, catalogued, and reused. The generic workstation is made domain specific by specialization of the user interface, capturing engineering design expertise for the domain, and by constructing/using a library of pertinent information. The incorporation of software reusability principles and expert system technology into this workstation provide the obvious benefits of increased productivity, improved software use and design reliability, and enhanced engineering quality by bringing engineering to higher levels of abstraction based on a well tested and classified library.

Automated analysis of biological oscillator models using mode decomposition.

PubMed

Konopka, Tomasz

2011-04-01

Oscillating signals produced by biological systems have shapes, described by their Fourier spectra, that can potentially reveal the mechanisms that generate them. Extracting this information from measured signals is interesting for the validation of theoretical models, discovery and classification of interaction types, and for optimal experiment design. An automated workflow is described for the analysis of oscillating signals. A software package is developed to match signal shapes to hundreds of a priori viable model structures defined by a class of first-order differential equations. The package computes parameter values for each model by exploiting the mode decomposition of oscillating signals and formulating the matching problem in terms of systems of simultaneous polynomial equations. On the basis of the computed parameter values, the software returns a list of models consistent with the data. In validation tests with synthetic datasets, it not only shortlists those model structures used to generate the data but also shows that excellent fits can sometimes be achieved with alternative equations. The listing of all consistent equations is indicative of how further invalidation might be achieved with additional information. When applied to data from a microarray experiment on mice, the procedure finds several candidate model structures to describe interactions related to the circadian rhythm. This shows that experimental data on oscillators is indeed rich in information about gene regulation mechanisms. The software package is available at http://babylone.ulb.ac.be/autoosc/.

Semi-automated sorting using holographic optical tweezers remotely controlled by eye/hand tracking camera

NASA Astrophysics Data System (ADS)

Tomori, Zoltan; Keša, Peter; Nikorovič, Matej; Kaůka, Jan; Zemánek, Pavel

2016-12-01

We proposed the improved control software for the holographic optical tweezers (HOT) proper for simple semi-automated sorting. The controller receives data from both the human interface sensors and the HOT microscope camera and processes them. As a result, the new positions of active laser traps are calculated, packed into the network format and sent to the remote HOT. Using the photo-polymerization technique, we created a sorting container consisting of two parallel horizontal walls where one wall contains "gates" representing a place where the trapped particle enters into the container. The positions of particles and gates are obtained by image analysis technique which can be exploited to achieve the higher level of automation. Sorting is documented on computer game simulation and the real experiment.

An Automated, High-Throughput System for GISAXS and GIWAXS Measurements of Thin Films

NASA Astrophysics Data System (ADS)

Schaible, Eric; Jimenez, Jessica; Church, Matthew; Lim, Eunhee; Stewart, Polite; Hexemer, Alexander

Grazing incidence small-angle X-ray scattering (GISAXS) and grazing incidence wide-angle X-ray scattering (GIWAXS) are important techniques for characterizing thin films. In order to meet rapidly increasing demand, the SAXSWAXS beamline at the Advanced Light Source (beamline 7.3.3) has implemented a fully automated, high-throughput system to conduct SAXS, GISAXS and GIWAXS measurements. An automated robot arm transfers samples from a holding tray to a measurement stage. Intelligent software aligns each sample in turn, and measures each according to user-defined specifications. Users mail in trays of samples on individually barcoded pucks, and can download and view their data remotely. Data will be pipelined to the NERSC supercomputing facility, and will be available to users via a web portal that facilitates highly parallelized analysis.

Instrumentation Automation for Concrete Structures: Report 2, Automation Hardware and Retrofitting Techniques, and Report 3, Available Data Collection and Reduction Software

DTIC Science & Technology

1987-06-01

commercial products. · OP -- Typical cutout at a plumbiinc location where an automated monitoring system has bv :• installed. The sensor used with the...This report provides a description of commercially available sensors , instruments, and ADP equipment that may be selected to fully automate...automated. The automated plumbline monitoring system includes up to twelve sensors , repeaters, a system controller, and a printer. The system may

Automated UHPLC separation of 10 pharmaceutical compounds using software-modeling.

PubMed

Zöldhegyi, A; Rieger, H-J; Molnár, I; Fekhretdinova, L

2018-03-20

Human mistakes are still one of the main reasons of underlying regulatory affairs that in a compliance with FDA's Data Integrity and Analytical Quality by Design (AQbD) must be eliminated. To develop smooth, fast and robust methods that are free of human failures, a state-of-the-art automation was presented. For the scope of this study, a commercial software (DryLab) and a model mixture of 10 drugs were subjected to testing. Following AQbD-principles, the best available working point was selected and conformational experimental runs, i.e. the six worst cases of the conducted robustness calculation, were performed. Simulated results were found to be in excellent agreement with the experimental ones, proving the usefulness and effectiveness of an automated, software-assisted analytical method development. Copyright © 2018. Published by Elsevier B.V.

Software support in automation of medicinal product evaluations.

PubMed

Juric, Radmila; Shojanoori, Reza; Slevin, Lindi; Williams, Stephen

2005-01-01

Medicinal product evaluation is one of the most important tasks undertaken by government health departments and their regulatory authorities, in every country in the world. The automation and adequate software support are critical tasks that can improve the efficiency and interoperation of regulatory systems across the world. In this paper we propose a software solution that supports the automation of the (i) submission of licensing applications, and (ii) evaluations of submitted licensing applications, according to regulatory authorities' procedures. The novelty of our solution is in allowing licensing applications to be submitted in any country in the world and evaluated according to any evaluation procedure (which can be chosen by either regulatory authorities or pharmaceutical companies). Consequently, submission and evaluation procedures become interoperable and the associated data repositories/databases can be shared between various countries and regulatory authorities.

Comparison of Automated Atlas-Based Segmentation Software for Postoperative Prostate Cancer Radiotherapy

PubMed Central

Delpon, Grégory; Escande, Alexandre; Ruef, Timothée; Darréon, Julien; Fontaine, Jimmy; Noblet, Caroline; Supiot, Stéphane; Lacornerie, Thomas; Pasquier, David

2016-01-01

Automated atlas-based segmentation (ABS) algorithms present the potential to reduce the variability in volume delineation. Several vendors offer software that are mainly used for cranial, head and neck, and prostate cases. The present study will compare the contours produced by a radiation oncologist to the contours computed by different automated ABS algorithms for prostate bed cases, including femoral heads, bladder, and rectum. Contour comparison was evaluated by different metrics such as volume ratio, Dice coefficient, and Hausdorff distance. Results depended on the volume of interest showed some discrepancies between the different software. Automatic contours could be a good starting point for the delineation of organs since efficient editing tools are provided by different vendors. It should become an important help in the next few years for organ at risk delineation. PMID:27536556

Performance Analysis of Automated Attack Graph Generation Software

DTIC Science & Technology

2006-12-01

MIT Lincoln Laboratory – NetSPA .................................................13 3. Skybox - Skybox View...Lip05*) 3. Skybox - Skybox View Skybox View is a commercially available tool developed by Skybox Security that can automatically generate...each host. It differs from CAULDRON because it requires that Skybox View probe live networks and must be connected to live networks during its

TBell: A mathematical tool for analyzing decision tables

NASA Technical Reports Server (NTRS)

Hoover, D. N.; Chen, Zewei

1994-01-01

This paper describes the development of mathematical theory and software to analyze specifications that are developed using decision tables. A decision table is a tabular format for specifying a complex set of rules that chooses one of a number of alternative actions. The report also describes a prototype tool, called TBell, that automates certain types of analysis.