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Generic software framework for a Line-Buffer-Based Image Processing Pipeline

IEEE TRANSACTIONS ON CONSUMER ELECTRONICS 2011年第3期57卷 1442-1449页

作者： Maatta, Joni-Matti Vanne, Jarno Hamalainen, Timo D. Nikkanen, Jarno Tampere Univ Technol Dept Comp Syst FI-33101 Tampere Finland Nokia Electr Ltd Tampere 33720 Finland

The majority of the current affordable mobile devices contain a camera with simple optics and a low-cost camera sensor. In these devices, the quality of the captured images is made acceptable with various image processing algorithms that together form an image reconstruction pipeline. The best performance is often achieved with a hardware pipeline, but software implementations can be preferred to minimize production costs and to maximize flexibility. This paper presents a generic software framework for a line-buffer-based image reconstruction pipeline. The presented framework is capable of operating in low-memory environments and significantly eases algorithm insertions, changes of processing order, and other pipeline management tasks. The savings in development time can be even months. In addition, our experiments show that it offers over 99% memory savings compared with traditional implementations using a ping-pong buffer scheme with full-sized image buffers. The implemented framework also enhances processing performance due to better cache usage and increases flexibility with various pipeline configurations(1).

关键词： software framework image reconstruction pipeline line buffer memory management

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A software framework for the Analysis of Complex Microscopy Image Data

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IEEE TRANSACTIONS ON INFORMATION TECHNOLOGY IN BIOMEDICINE 2010年第4期14卷 1075-1087页

作者： Chao, Jerry Ward, E. Sally Ober, Raimund J. Univ Texas Dallas Dept Elect Engn Richardson TX 75080 USA Univ Texas SW Med Ctr Dallas Dept Immunol Dallas TX 75390 USA

Technological advances in both hardware and software have made possible the realization of sophisticated biological imaging experiments using the optical microscope. As a result, modern microscopy experiments are capable of producing complex image datasets. For a given data analysis task, the images in a set are arranged, based on the requirements of the task, by attributes such as the time and focus levels at which they were acquired. Importantly, different tasks performed over the course of an analysis are often facilitated by the use of different arrangements of the images. We present a software framework that supports the use of different logical image arrangements to analyze a physical set of images. This framework, called the Microscopy Image Analysis Tool (MIATool), realizes the logical arrangements using arrays of pointers to the images, thereby removing the need to replicate and manipulate the actual images in their storage medium. In order that they may be tailored to the specific requirements of disparate analysis tasks, these logical arrangements may differ in size and dimensionality, with no restrictions placed on the number of dimensions and the meaning of each dimension. MIATool additionally supports processing flexibility, extensible image processing capabilities, and data storage management.

关键词： Image analysis image viewer microscopy multidimensional data software framework

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A Health Surveillance software framework to deliver information on preventive healthcare strategies

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JOURNAL OF BIOMEDICAL INFORMATICS 2016年 62卷 159-170页

作者： Macedo, Alessandra Alaniz Pollettini, Juliana Tarossi Baranauskas, Jose Augusto Almeida Chaves, Julia Carmona Univ Sao Paulo Dept Comp Sci & Math Biomed Informat Grp Av Bandeirantes 3900 BR-14040901 Ribeirao Preto SP Brazil

A software framework can reduce costs related to the development of an application because it allows developers to reuse both design and code. Recently, companies and research groups have announced that they have been employing health software frameworks. This paper presents the design, proof-of-concept implementations and experimentation of the Health Surveillance software framework (HSSF). The HSSF is a framework that tackles the demand for the recommendation of surveillance information aiming at supporting preventive healthcare strategies. Examples of such strategies are the automatic recommendation of surveillance levels to patients in need of healthcare and the automatic recommendation of scientific literature that elucidates epigenetic problems related to patients. HSSF was created from two systems we developed in our previous work on health surveillance systems: the Automatic-SL and CISS systems. The Automatic-SL system aims to assist healthcare professionals in making decisions and in identifying children with developmental problems. The CISS service associates genetic and epigenetic risk factors related to chronic diseases with patient's clinical records. Towards evaluating the HSSF framework, two new systems, CISS+ and CISS-SW, were created by means of abstractions and instantiations of the framework (design and code). We show that HSSF supported the development of the two new systems given that they both recommend scientific papers using medical records as queries even though they exploit different computational technologies. In an experiment using simulated patients' medical records, we show that CISS, CISS+, and CISS-SW systems recommended more closely related and somewhat related documents than Google, Google Scholar and PubMed. Considering recall and precision measures, CISS+ surpasses CISS-SW in terms of precision. (C) 2016 Elsevier Inc. All rights reserved.

关键词： software framework Reuse Biomedical informatics Information extraction Retrieval and application of biomedical knowledge and information Recommender systems: medical records and scientific papers Ontology

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GNU polyxmass: a software framework for mass spectrometric simulations of linear (bio-)polymeric analytes

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BMC BIOINFORMATICS 2006年第1期7卷 1-16页

作者： Rusconi, Filippo CNRS UMR5153 F-75231 Paris France INSERM U565 F-75231 Paris France Museum Natl Hist Nat Mass Spectrometry Facil USM0503 F-75231 Paris France

Background: Nowadays, a variety of ( bio-) polymers can be analyzed by mass spectrometry. The detailed interpretation of the spectra requires a huge number of "hypothesis cycles", comprising the following three actions 1) put forth a structural hypothesis, 2) test it, 3) ( in) validate it. This time-consuming and painstaking data scrutiny is alleviated by using specialized software tools. However, all the software tools available to date are polymer chemistry-specific. This imposes a heavy overhead to researchers who do mass spectrometry on a variety of ( bio-) polymers, as each polymer type will require a different software tool to perform data simulations and analyses. We developed a software to address the lack of an integrated software framework able to deal with different polymer chemistries. Results: The GNU polyxmass software framework performs common ( bio-) chemical simulations along with simultaneous mass spectrometric calculations - for any kind of linear bio- polymeric analyte ( DNA, RNA, saccharides or proteins). The framework is organized into three modules, all accessible from one single binary program. The modules let the user to 1) define brand new polymer chemistries, 2) perform quick mass calculations using a desktop calculator paradigm, 3) graphically edit polymer sequences and perform ( bio-) chemical/mass spectrometric simulations. Any aspect of the mass calculations, polymer chemistry reactions or graphical polymer sequence editing is configurable. Conclusion: The scientist who uses mass spectrometry to characterize ( bio-) polymeric analytes of different chemistries is provided with a single software framework for his data prediction/ analysis needs, whatever the polymer chemistry being involved.

关键词： Polymer Chemistry Cyanogen Bromide software framework Sequence Editor Scalar Vector Graphic

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The Communication Layer of the aRDx software framework: Highly Performant and Realtime Deterministic

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JOURNAL OF INTELLIGENT & ROBOTIC SYSTEMS 2015年第1期77卷 171-185页

作者： Hammer, Tobias Baeuml, Berthold DLR Inst Robot & Mechatron D-82234 Wessling Germany

Communication between software components is one of the most important functionalities a software framework for modern complex robotic systems has to provide. Here, we present the highly performant realtime communication layer of our new robotic software framework aRDx (agile robot development - next generation), with, e.g., zero-copy semantics, realtime determinism and detailed control of the QoS (quality of service). In addition, we give an in- depth performance comparison to other popular robotic frameworks, namely ROS, YARP, Orocos and aRD.

关键词： software framework Robotics Realtime Performant communication

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ESFM: An Essential software framework for Meshfree Methods

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ADVANCES IN ENGINEERING software 2014年 76卷 133-147页

作者： Hsieh, Yo-Ming Pan, Mao-Sen Natl Taiwan Univ Sci & Technol Dept Construct Engn Taipei Taiwan

This paper describes an Essential software framework for Meshfree Methods (ESFM). Through thorough analyses of many existing meshfree methods, their common elements and procedures are identified, and a general procedure is formulated into ESFM that can facilitate their implementations and accelerate new developments in meshfree methods. ESFM also modulates performance-critical components such as neighbor-point searching, sparse-matrix storage, and sparse-matrix solver enabling developed meshfree analysis programs to achieve high-performance. ESFM currently consists of 21 groups of classes and 94 subclasses, and more algorithms can be easily incorporated into ESFM. Finally, ESFM provides a common ground to compare various meshfree methods, enabling detailed analyses of performance characteristics. (C) 2014 Elsevier Ltd. All rights reserved.

关键词： Meshfree methods Meshless methods software framework Object-oriented design Design pattern Weak-form

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A software framework for KM3NeT

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NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH SECTION A-ACCELERATORS SPECTROMETERS DETECTORS AND ASSOCIATED EQUIPMENT 2009年第1期602卷 107-110页

作者： Kopper, Claudio Univ Erlangen Nurnberg ECAP D-91058 Erlangen Germany

Modular software frameworks have become indispensable for large-scale experiments like the KM3NCT neutrino telescope. This article gives a generic definition of a software framework and presents an adaptation of IceTray, the framework currently in use by the IceCube collaboration, for water-based detectors. (C) 2009 Elsevier B.V. All rights reserved.

关键词： KM3NeT software framework IceTray IceCube Analysis software

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A software framework for fine grain parallelization of cellular models with OpenMP: Application to fire spread

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ENVIRONMENTAL MODELLING & software 2009年第7期24卷 819-831页

作者： Innocenti, Eric Silvani, Xavier Muzy, Alexandre Hill, David R. C. Univ Blaise Pascal ISIMA LIMOS CNRS UMR 6158 F-63177 Aubiere France Univ Cors CNRS SPE UMR 6134 F-20250 Corte France

We are dealing here with the parallelization of fire spreading simulations following detailed physical experiments. The proposal presented in this paper has been tested and evaluated in collaboration with physicists to meet their requirements in terms of both performance and precision. For this purpose, an object-oriented framework using two abstraction levels has been developed. A first level considers the simulation as a global phenomenon which evolves in space and time. A local level describes the phenomena occurring on elementary parts of the domain. In order to develop an extensible and modular architecture, the cellular automata paradigm, the DEVS discrete event system formalism and design patterns have been used. Simulation treatments are limited to a set of active elements to improve execution times. A new kind of model, called Active-DEVS is then specified. The model is computed with a fine grain parallelization very efficient for present day multi-core processors which are elementary units of modern computing clusters and computing grids. In this paper, the parallelization with Open MultiProcessing (OpenMP) standard directives on Symmetric MultiProcessing (SMP) architectures is discussed and the efficiency of the retained Solution is studied. (C) 2008 Published by Elsevier Ltd.

关键词： software framework Fire spread physical model DEVS Open MultiProcessing (OpenMP) Symmetric multiprocessors (SMP)

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MAPI: a software framework for distributed biomedical applications

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JOURNAL OF BIOMEDICAL SEMANTICS 2013年第1期4卷 1-12页

作者： Karlsson, Johan Trelles, Oswaldo Univ Malaga Comp Architecture Dept Malaga 29080 Spain

Background: The amount of web-based resources (databases, tools etc.) in biomedicine has increased, but the integrated usage of those resources is complex due to differences in access protocols and data formats. However, distributed data processing is becoming inevitable in several domains, in particular in biomedicine, where researchers face rapidly increasing data sizes. This big data is difficult to process locally because of the large processing, memory and storage capacity required. Results: This manuscript describes a framework, called MAPI, which provides a uniform representation of resources available over the Internet, in particular for Web Services. The framework enhances their interoperability and collaborative use by enabling a uniform and remote access. The framework functionality is organized in modules that can be combined and configured in different ways to fulfil concrete development requirements. Conclusions: The framework has been tested in the biomedical application domain where it has been a base for developing several clients that are able to integrate different web resources. The MAPI binaries and documentation are freely available at http://***/mapi under the Creative Commons Attribution-No Derivative Works 2.5 Spain License. The MAPI source code is available by request (GPL v3 license).

关键词： Service-oriented architectures Web-service integration software framework

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Surgical model-view-controller simulation software framework for local and collaborative applications

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INTERNATIONAL JOURNAL OF COMPUTER ASSISTED RADIOLOGY AND SURGERY 2011年第4期6卷 457-471页

作者： Maciel, Anderson Sankaranarayanan, Ganesh Halic, Tansel Arikatla, Venkata Sreekanth Lu, Zhonghua De, Suvranu Univ Fed Rio Grande do Sul Inst Informat BR-91501970 Porto Alegre RS Brazil Rensselaer Polytech Inst Troy NY 12180 USA

Purpose Surgical simulations require haptic interactions and collaboration in a shared virtual environment. A software framework for decoupled surgical simulation based on a multi-controller and multi-viewer model-view-controller (MVC) pattern was developed and tested. Methods A software framework for multimodal virtual environments was designed, supporting both visual interactions and haptic feedback while providing developers with an integration tool for heterogeneous architectures maintaining high performance, simplicity of implementation, and straightforward extension. The framework uses decoupled simulation with updates of over 1,000 Hz for haptics and accommodates networked simulation with delays of over 1,000 ms without performance penalty. Results The simulation software framework was implemented and was used to support the design of virtual reality-based surgery simulation systems. The framework supports the high level of complexity of such applications and the fast response required for interaction with haptics. The efficacy of the framework was tested by implementation of a minimally invasive surgery simulator. Conclusion A decoupled simulation approach can be implemented as a framework to handle simultaneous processes of the system at the various frame rates each process requires. The framework was successfully used to develop collaborative virtual environments (VEs) involving geographically distributed users connected through a network, with the results comparable to VEs for local users.

关键词： Surgical simulation Virtual environments Physics-based simulation User interfaces-Haptic I/O software framework

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