MIA - a free and open source software for gray scale medical image analysis

Background Gray scale images make the bulk of data in bio-medical image analysis, and hence, the main focus of many image processing tasks lies in the processing of these monochrome images. With ever improving acquisition devices, spatial and temporal image resolution increases, and data sets become very large. Various image processing frameworks exists that make the development of new algorithms easy by using high level programming languages or visual programming. These frameworks are also accessable to researchers that have no background or little in software development because they take care of otherwise complex tasks. Specifically, the management of working memory is taken care of automatically, usually at the price of requiring more it. As a result, processing large data sets with these tools becomes increasingly difficult on work station class computers. One alternative to using these high level processing tools is the development of new algorithms in a languages like C++, that gives the developer full control over how memory is handled, but the resulting workflow for the prototyping of new algorithms is rather time intensive, and also not appropriate for a researcher with little or no knowledge in software development. Another alternative is in using command line tools that run image processing tasks, use the hard disk to store intermediate results, and provide automation by using shell scripts. Although not as convenient as, e.g. visual programming, this approach is still accessable to researchers without a background in computer science. However, only few tools exist that provide this kind of processing interface, they are usually quite task specific, and don’t provide an clear approach when one wants to shape a new command line tool from a prototype shell script. Results The proposed framework, MIA, provides a combination of command line tools, plug-ins, and libraries that make it possible to run image processing tasks interactively in a command shell and to prototype by using the according shell scripting language. Since the hard disk becomes the temporal storage memory management is usually a non-issue in the prototyping phase. By using string-based descriptions for filters, optimizers, and the likes, the transition from shell scripts to full fledged programs implemented in C++ is also made easy. In addition, its design based on atomic plug-ins and single tasks command line tools makes it easy to extend MIA, usually without the requirement to touch or recompile existing code. Conclusion In this article, we describe the general design of MIA, a general purpouse framework for gray scale image processing. We demonstrated the applicability of the software with example applications from three different research scenarios, namely motion compensation in myocardial perfusion imaging, the processing of high resolution image data that arises in virtual anthropology, and retrospective analysis of treatment outcome in orthognathic surgery. With MIA prototyping algorithms by using shell scripts that combine small, single-task command line tools is a viable alternative to the use of high level languages, an approach that is especially useful when large data sets need to be processed.

Modification and Developer Metrics at the Function Level: Metrics for the Study of the Evolution of a Software Project

Software evolution, and particularly its growth, has been mainly studied at the file (also sometimes referred as module) level. In this paper we propose to move from the physical towards a level that includes semantic information by using functions or methods for measuring the evolution of a software system. We point out that use of functions-based metrics has many advantages over the use of files or lines of code. We demonstrate our approach with an empirical study of two Free/Open Source projects: a community-driven project, Apache, and a company-led project, Novell Evolution. We discovered that most functions never change; when they do their number of modifications is correlated with their size, and that very few authors who modify each; finally we show that the departure of a developer from a software project slows the evolution of the functions that she authored.

Quantitative Determination of the Relationship between Internal Validity and Bias in Software Engineering Experiments: Consequences for Systematic Literature Reviews

Quality assessment is one of the activities performed as part of systematic literature reviews. It is commonly accepted that a good quality experiment is bias free. Bias is considered to be related to internal validity (e.g., how adequately the experiment is planned, executed and analysed). Quality assessment is usually conducted using checklists and quality scales. It has not yet been proven;however, that quality is related to experimental bias. Aim: Identify whether there is a relationship between internal validity and bias in software engineering experiments. Method: We built a quality scale to determine the quality of the studies, which we applied to 28 experiments included in two systematic literature reviews. We proposed an objective indicator of experimental bias, which we applied to the same 28 experiments. Finally, we analysed the correlations between the quality scores and the proposed measure of bias. Results: We failed to find a relationship between the global quality score (resulting from the quality scale) and bias; however, we did identify interesting correlations between bias and some particular aspects of internal validity measured by the instrument. Conclusions: There is an empirically provable relationship between internal validity and bias. It is feasible to apply quality assessment in systematic literature reviews, subject to limits on the internal validity aspects for consideration.

Studying the laws of software evolution in a long-lived FLOSS project

ome free, open-source software projects have been around for quite a long time, the longest living ones dating from the early 1980s. For some of them, detailed information about their evolution is available in source code management systems tracking all their code changes for periods of more than 15 years. This paper examines in detail the evolution of one of such projects, glibc, with the main aim of understanding how it evolved and how it matched Lehman's laws of software evolution. As a result, we have developed a methodology for studying the evolution of such long-lived projects based on the information in their source code management repository, described in detail several aspects of the history of glibc, including some activity and size metrics, and found how some of the laws of software evolution may not hold in this case

UBURYO: open source software for managing microcredits in education

One of the major problems in developing countries is minority access to higher education. Traditional scholarships usually focus on paying tuition fees for bringing brilliant students to developed countries (from where they seldom return). But local grants seldom target the more needy students. We propose a system of student loans to pay tuition fees in exchange for technical work. This appears to be a satisfactory and sustainable solution. We also provide UBURYO (a Kirundi word meaning opportunity). UBURYO is the free open source software, that we have developed, to manage this loan system in a simple, trustworthy, fair and efficient way.

Determining the effectiveness of three software evaluation techniques through informal aggregation

An accepted fact in software engineering is that software must undergo verification and validation process during development to ascertain and improve its quality level. But there are too many techniques than a single developer could master, yet, it is impossible to be certain that software is free of defects. So, it is crucial for developers to be able to choose from available evaluation techniques, the one most suitable and likely to yield optimum quality results for different products. Though, some knowledge is available on the strengths and weaknesses of the available software quality assurance techniques but not much is known yet on the relationship between different techniques and contextual behavior of the techniques. Objective: This research investigates the effectiveness of two testing techniques ? equivalence class partitioning and decision coverage and one review technique ? code review by abstraction, in terms of their fault detection capability. This will be used to strengthen the practical knowledge available on these techniques.

Estudio comparativo y completo de la oferta de software libre para centros de educación primaria

La Organización de Estados Iberoamericanos para la Educación, la Ciencia y la Cultura (OEI) pretende llevar energía solar y acceso a internet a más de 66.000 escuelas en Iberoamérica, la mayor parte de ellas ubicadas en zonas rurales y de difícil acceso. Con el proyecto “Luces para aprender” se quiere reducir la brecha digital y poner fin al aislamiento de las comunidades rurales, facilitando su acceso a las tecnologías de la comunicación, con el fin de favorecer su desarrollo educativo, económico, social y cultural. La OEI que coordina el proyecto “Luces para Aprender” se dirigió a TEDECO (Tecnología para el Desarrollo y la Cooperación), que es un grupo de cooperación al desarrollo de la Facultad de Informática de la UPM, para solicitar asesoramiento en la parte software a instalar en el proyecto. Surge la necesidad de dotar de sistema operativo a los computadores que tendrán las escuelas beneficiarias de este proyecto. Por lo tanto, se ha decido crear un sistema operativo que consiste en una distribución GNU/Linux que se adapte a las necesidades de dicho proyecto. Esta distribución va acompañada de un manual de usuario y una guía de instalación para facilitar la implantación en los respectivos centros. Se pretende que la distribución esté disponible en un repositorio web y además esté basada en la filosofía de código libre y abierto. ---ABSTRACT---The OEI (Organization of Ibero-American States for Education, Science and Culture) hopes to provide solar energy and Internet access to more than 66.000 schools in Ibero-America, most of them, located in rural zones and of difficult access. With the project “Luces para aprender” (lights to learn), they would like to reduce the digital gap and put an end to the deprivation of the rural communities, supplying access to the Information Technologies, with the aim of contributing to its educative, economic, social and cultural development. The OEI that coordinates "Luces para Apreder" project, requested TEDECO (Technology for Development and Cooperation), which is a group of development cooperation of Facultad de Informática of the UPM, to advice in the part of software installation in the project. There is a need for an operative system that the computers will have in schools that will benefit from that project. Therefore, it has been decided to create an operative system that consists of a GNU/Linux distribution adapted to the needs of the project. That distribution will be accompanied by a user’s manual and an installation guide to help the implementing in the centres. The distribution is supposed to be available in a web, and moreover, will be based on the philosophy of free and opened codes.

On the acquisition of high-resolution maps with open source software and commercials off-the-shelf quad-rotors

Mosaics are high-resolution images obtained aerially and employed in several scientific research areas, such for example, in the field of environmental monitoring and precision agriculture. Although many high resolution maps are obtained by commercial demand, they can also be acquired with commercial aerial vehicles which provide more experimental autonomy and availability. For what regard to mosaicing-based aerial mission planners, there are not so many - if any - free of charge software. Therefore, in this paper is presented a framework designed with open source tools and libraries as an alternative to commercial tools to carry out mosaicing tasks.