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.

Open Source website

La idea de este proyecto es acercar la imagen de Libertad de Información y su conocida variante Open Source, donde cubriremos en detalle la multitud de puntos que abarca. Está dirigida a todos los usuarios que quieran conocer de primera mano cómo se inició la idea de Libertad Tecnológica hasta sus aplicaciones. No solo para aquellos que quieran emplearla, sino tambien para aquellos que la ya la usan y necesitan recursos para nuevas ideas. De esta forma, nos acercaremos tambien a la idea de libertad que en la tecnología está actualmente en debate. El contenido se estructura siguiendo las siguientes ramas:  Historia, desde sus orígenes hasta el presente.  Economía, ventajas y desventajas de esta libertad.  Problemas legales en distintos niveles  Noticias y actualizaciones de aplicaciones.  Sociedad, entorno a la aceptación y rechazo por los usuarios, ademas de su influencia en la ética, educación e innovación.  Aplicaciones, donde se incluirán la mayoría de las aplicaciones más conocidas en cada una de las ramas de Open Source. ---ABSTRACT---The topic finally chosen in the list of Professional Skills and Issues has been the Freedom of Information and its best known variant Open Source. We will try to cover in detail most of the points that includes history, economics, law, society and the various applications in which it have influenced. It allows all the public to see first-hand the term of Open Source, from its beginnings to applications. Not just for those who want to use it, but for those who already use it and want to find sources and new ideas. It will also get a step closer to the idea of Freedom of Information as currently being debated. The main branches are going to address:  History, from its origins to the present.  Economic, advantages and disadvantages of being free.  Laws, problems in different continents at the legal level.  News, latest in its various applications.  Society, acceptance or rejection by the people, addition to the factors that influence as ethics, education, and arts innovation.  Applications, where most try to include most current applications of each of the variants.

Crowdsourcing de información geográfica: proyectos Open Source y desarrollo de una plataforma móvil para mantenimiento de infraestructura urbana.

El presente trabajo se centra en la investigación del modelo de crowdsourcing y su relación con la Información Geográfica Voluntaria y otras actividades participativas para la creación de conocimiento geográfico de forma colaborativa. Primero se expone una introducción al concepto y distintos ámbitos de aplicación y uso en la adquisición,visualización y análisis de datos geográficos, presentándose las herramientas, tecnologías web y móviles que han hecho posible su implementación. Después se hace una breve revisión de algunas plataformas de código abierto que faciliten la creación de contenido geolocalizado por el usuario y proporcionen funcionalidades para el análisis básico y manipulación de información mediante la implementación de estrategias de crowdsourcing. En los apartados siguientes, se hace un breve análisis de requisitos para el caso de uso específico de una aplicación móvil de crowdsourcing para el mantenimiento urbano, sirviendo este, como base en el desarrollo de una plataforma Web-móvil que facilite la gestión de este tipo de infraestructura. El diseño de la plataforma propuesta permite consultar y actualizar información por medio de etiquetas NFC (Near Field Communications o comunicación de campo cercano) utilizadas en el mobiliario urbano inventariado y empleando dispositivos inteligentes habilitados con la misma tecnología y conexión a Internet, para dar seguimiento y reportar el estado de la infraestructura. También, es posible generar reportes geolocalizados sobre problemas en instalaciones urbanas no inventariadas, así como crear eventos geolocalizados que convoquen a tareas participativas para la mejora de la ciudad. Además, integra entradas de conversación de redes sociales para contribuir a la participación activa de los ciudadanos en la vigilancia y mantenimiento urbano. Por último, el trabajo presenta algunas conclusiones y líneas futuras.

Virtual science hub: an open source platform to enrich science teaching

This paper presents the Virtual Science Hub platform. It is an open source platform that combines a social network, an e-learning authoring tool, a videoconference service and a learning object repository for science teaching enrichment. These four main functionalities fit very well together. The platform was released in April 2012 and since then it has not stopped growing. Finally we present the results of the surveys conducted and the statistics gathered to validate this approach.

A flexible open source web platform to facilitate Learning Object evaluation

Systematic evaluation of Learning Objects is essential to make high quality Web-based education possible. For this reason, several educational repositories and e-Learning systems have developed their own evaluation models and tools. However, the differences of the context in which Learning Objects are produced and consumed suggest that no single evaluation model is sufficient for all scenarios. Besides, no much effort has been put in developing open tools to facilitate Learning Object evaluation and use the quality information for the benefit of end users. This paper presents LOEP, an open source web platform that aims to facilitate Learning Object evaluation in different scenarios and educational settings by supporting and integrating several evaluation models and quality metrics. The work exposed in this paper shows that LOEP is capable of providing Learning Object evaluation to e-Learning systems in an open, low cost, reliable and effective way. Possible scenarios where LOEP could be used to implement quality control policies and to enhance search engines are also described. Finally, we report the results of a survey conducted among reviewers that used LOEP, showing that they perceived LOEP as a powerful and easy to use tool for evaluating Learning Objects.

A proposal for an Internet of Things-based monitoring system composed by low capability, open source and open hardware devices

The Internet of Things makes use of a huge disparity of technologies at very different levels that help one to the other to accomplish goals that were previously regarded as unthinkable in terms of ubiquity or scalability. If the Internet of Things is expected to interconnect every day devices or appliances and enable communications between them, a broad range of new services, applications and products can be foreseen. For example, monitoring is a process where sensors have widespread use for measuring environmental parameters (temperature, light, chemical agents, etc.) but obtaining readings at the exact physical point they want to be obtained from, or about the exact wanted parameter can be a clumsy, time-consuming task that is not easily adaptable to new requirements. In order to tackle this challenge, a proposal on a system used to monitor any conceivable environment, which additionally is able to monitor the status of its own components and heal some of the most usual issues of a Wireless Sensor Network, is presented here in detail, covering all the layers that give it shape in terms of devices, communications or services.

A comparison of open-source segmentation architectures for dealing with imperfect data from the media in speech synthesis

Traditional Text-To-Speech (TTS) systems have been developed using especially-designed non-expressive scripted recordings. In order to develop a new generation of expressive TTS systems in the Simple4All project, real recordings from the media should be used for training new voices with a whole new range of speaking styles. However, for processing this more spontaneous material, the new systems must be able to deal with imperfect data (multi-speaker recordings, background and foreground music and noise), filtering out low-quality audio segments and creating mono-speaker clusters. In this paper we compare several architectures for combining speaker diarization and music and noise detection which improve the precision and overall quality of the segmentation.

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.

A Reliable Open-Source System Architecture for the Fast Designing and Prototyping of Autonomous Multi-UAV Systems: Simulation and Experimentation

During the process of design and development of an autonomous Multi-UAV System, two main problems appear. The first one is the difficulty of designing all the modules and behaviors of the aerial multi-robot system. The second one is the difficulty of having an autonomous prototype of the system for the developers that allows to test the performance of each module even in an early stage of the project. These two problems motivate this paper. A multipurpose system architecture for autonomous multi-UAV platforms is presented. This versatile system architecture can be used by the system designers as a template when developing their own systems. The proposed system architecture is general enough to be used in a wide range of applications, as demonstrated in the paper. This system architecture aims to be a reference for all designers. Additionally, to allow for the fast prototyping of autonomous multi-aerial systems, an Open Source framework based on the previously defined system architecture is introduced. It allows developers to have a flight proven multi-aerial system ready to use, so that they can test their algorithms even in an early stage of the project. The implementation of this framework, introduced in the paper with the name of “CVG Quadrotor Swarm”, which has also the advantages of being modular and compatible with different aerial platforms, can be found at https://​github.​com/​Vision4UAV/​cvg_​quadrotor_​swarm with a consistent catalog of available modules. The good performance of this framework is demonstrated in the paper by choosing a basic instance of it and carrying out simulation and experimental tests whose results are summarized and discussed in this paper.

Experiences Using an Open Source Sofware Library to Teach Computer Vision Subjects

Machine vision is an important subject in computer science and engineering degrees. For laboratory experimentation, it is desirable to have a complete and easy-to-use tool. In this work we present a Java library, oriented to teaching computer vision. We have designed and built the library from the scratch with enfasis on readability and understanding rather than on efficiency. However, the library can also be used for research purposes. JavaVis is an open source Java library, oriented to the teaching of Computer Vision. It consists of a framework with several features that meet its demands. It has been designed to be easy to use: the user does not have to deal with internal structures or graphical interface, and should the student need to add a new algorithm it can be done simply enough. Once we sketch the library, we focus on the experience the student gets using this library in several computer vision courses. Our main goal is to find out whether the students understand what they are doing, that is, find out how much the library helps the student in grasping the basic concepts of computer vision. In the last four years we have conducted surveys to assess how much the students have improved their skills by using this library.

Modelação espacial do potencial de produção apícola utilizando software open source

Modelação espacial do potencial de produção apícola utilizando software open source.

Ferramentas open source de Data Mining

Em época de crise financeira, as ferramentas open source de data mining representam uma nova tendência na investigação, educação e nas aplicações industriais, especialmente para as pequenas e médias empresas. Com o software open source, estas podem facilmente iniciar um projeto de data mining usando as tecnologias mais recentes, sem se preocuparem com os custos de aquisição das mesmas, podendo apostar na aprendizagem dos seus colaboradores. Os sistemas open source proporcionam o acesso ao código, facilitando aos colaboradores a compreensão dos sistemas e algoritmos e permitindo que estes o adaptem às necessidades dos seus projetos. No entanto, existem algumas questões inerentes ao uso deste tipo de ferramenta. Uma das mais importantes é a diversidade, e descobrir, tardiamente, que a ferramenta escolhida é inapropriada para os objetivos do nosso negócio pode ser um problema grave. Como o número de ferramentas de data mining continua a crescer, a escolha sobre aquela que é realmente mais apropriada ao nosso negócio torna-se cada vez mais difícil. O presente estudo aborda um conjunto de ferramentas de data mining, de acordo com as suas características e funcionalidades. As ferramentas abordadas provém da listagem do KDnuggets referente a Software Suites de Data Mining. Posteriormente, são identificadas as que reúnem melhores condições de trabalho, que por sua vez são as mais populares nas comunidades, e é feito um teste prático com datasets reais. Os testes pretendem identificar como reagem as ferramentas a cenários diferentes do tipo: performance no processamento de grandes volumes de dados; precisão de resultados; etc. Nos tempos que correm, as ferramentas de data mining open source representam uma oportunidade para os seus utilizadores, principalmente para as pequenas e médias empresas, deste modo, os resultados deste estudo pretendem ajudar no processo de tomada de decisão relativamente às mesmas.

Screening of the Open Source Malaria Box Reveals an Early Lead Compound for the Treatment of Alveolar Echinococcosis.

The metacestode (larval) stage of the tapeworm Echinococcus multilocularis causes alveolar echinococcosis (AE), a very severe and in many cases incurable disease. To date, benzimidazoles such as albendazole and mebendazole are the only approved chemotherapeutical treatment options. Benzimidazoles inhibit metacestode proliferation, but do not act parasiticidal. Thus, benzimidazoles have to be taken a lifelong, can cause adverse side effects such as hepatotoxicity, and are ineffective in some patients. We here describe a newly developed screening cascade for the evaluation of the in vitro efficacy of new compounds that includes assessment of parasiticidal activity. The Malaria Box from Medicines for Malaria Venture (MMV), comprised of 400 commercially available chemicals that show in vitro activity against Plasmodium falciparum, was repurposed. Primary screening was carried out at 10 μM by employing the previously described PGI assay, and resulted in the identification of 24 compounds that caused physical damage in metacestodes. Seven out of these 24 drugs were also active at 1 μM. Dose-response assays revealed that only 2 compounds, namely MMV665807 and MMV665794, exhibited an EC50 value below 5 μM. Assessments using human foreskin fibroblasts and Reuber rat hepatoma cells showed that the salicylanilide MMV665807 was less toxic for these two mammalian cell lines than for metacestodes. The parasiticidal activity of MMV665807 was then confirmed using isolated germinal layer cell cultures as well as metacestode vesicles by employing viability assays, and its effect on metacestodes was morphologically evaluated by electron microscopy. However, both oral and intraperitoneal application of MMV665807 to mice experimentally infected with E. multilocularis metacestodes did not result in any reduction of the parasite load.

Bibliography of intelligence literature : a critical and annotated bibliography of open-source literature

Mode of access: Internet.

Open-Source Computerized Patient-Reported Outcomes: Case Studies Illustrating Fifteen Years of Evolution

Thesis (Master's)--University of Washington, 2016-06