Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities.

/pdf/fiji-an-open-source-platform-for-biological-image-analysis-1v529iu3cx.pdf

Fiji: an open-source platform for biological-image analysis

ImageJ is an image analysis program extensively used in the biological sciences and beyond. Due to its ease of use, recordable macro language, and extensible plug-in architecture, ImageJ enjoys contributions from non-programmers, amateur programmers, and professional developers alike. Enabling such a diversity of contributors has resulted in a large community that spans the biological and physical sciences. However, a rapidly growing user base, diverging plugin suites, and technical limitations have revealed a clear need for a concerted software engineering effort to support emerging imaging paradigms, to ensure the software’s ability to handle the requirements of modern science. We rewrote the entire ImageJ codebase, engineering a redesigned plugin mechanism intended to facilitate extensibility at every level, with the goal of creating a more powerful tool that continues to serve the existing community while addressing a wider range of scientific requirements. This next-generation ImageJ, called “ImageJ2” in places where the distinction matters, provides a host of new functionality. It separates concerns, fully decoupling the data model from the user interface. It emphasizes integration with external applications to maximize interoperability. Its robust new plugin framework allows everything from image formats, to scripting languages, to visualization to be extended by the community. The redesigned data model supports arbitrarily large, N-dimensional datasets, which are increasingly common in modern image acquisition. Despite the scope of these changes, backwards compatibility is maintained such that this new functionality can be seamlessly integrated with the classic ImageJ interface, allowing users and developers to migrate to these new methods at their own pace. Scientific imaging benefits from open-source programs that advance new method development and deployment to a diverse audience. ImageJ has continuously evolved with this idea in mind; however, new and emerging scientific requirements have posed corresponding challenges for ImageJ’s development. The described improvements provide a framework engineered for flexibility, intended to support these requirements as well as accommodate future needs. Future efforts will focus on implementing new algorithms in this framework and expanding collaborations with other popular scientific software suites.

/pdf/imagej2-imagej-for-the-next-generation-of-scientific-image-41ybjcosb6.pdf

ImageJ2: ImageJ for the next generation of scientific image data

In this paper, we review the background and state-of-the-art of big data. We first introduce the general background of big data and review related technologies, such as could computing, Internet of Things, data centers, and Hadoop. We then focus on the four phases of the value chain of big data, i.e., data generation, data acquisition, data storage, and data analysis. For each phase, we introduce the general background, discuss the technical challenges, and review the latest advances. We finally examine the several representative applications of big data, including enterprise management, Internet of Things, online social networks, medial applications, collective intelligence, and smart grid. These discussions aim to provide a comprehensive overview and big-picture to readers of this exciting area. This survey is concluded with a discussion of open problems and future directions.

Big Data: A Survey

ImageJ is an image analysis program extensively used in the biological sciences and beyond. Due to its ease of use, recordable macro language, and extensible plug-in architecture, ImageJ enjoys contributions from non-programmers, amateur programmers, and professional developers alike. Enabling such a diversity of contributors has resulted in a large community that spans the biological and physical sciences. However, a rapidly growing user base, diverging plugin suites, and technical limitations have revealed a clear need for a concerted software engineering effort to support emerging imaging paradigms, to ensure the software's ability to handle the requirements of modern science. Due to these new and emerging challenges in scientific imaging, ImageJ is at a critical development crossroads. 
We present ImageJ2, a total redesign of ImageJ offering a host of new functionality. It separates concerns, fully decoupling the data model from the user interface. It emphasizes integration with external applications to maximize interoperability. Its robust new plugin framework allows everything from image formats, to scripting languages, to visualization to be extended by the community. The redesigned data model supports arbitrarily large, N-dimensional datasets, which are increasingly common in modern image acquisition. Despite the scope of these changes, backwards compatibility is maintained such that this new functionality can be seamlessly integrated with the classic ImageJ interface, allowing users and developers to migrate to these new methods at their own pace. ImageJ2 provides a framework engineered for flexibility, intended to support these requirements as well as accommodate future needs.

Technology in microscopy advances rapidly, enabling increasingly affordable, faster, and more precise quantitative biomedical imaging, which necessitates correspondingly more-advanced image processing and analysis techniques. A wide range of software is available-from commercial to academic, special-purpose to Swiss army knife, small to large-but a key characteristic of software that is suitable for scientific inquiry is its accessibility. Open-source software is ideal for scientific endeavors because it can be freely inspected, modified, and redistributed; in particular, the open-software platform ImageJ has had a huge impact on the life sciences, and continues to do so. From its inception, ImageJ has grown significantly due largely to being freely available and its vibrant and helpful user community. Scientists as diverse as interested hobbyists, technical assistants, students, scientific staff, and advanced biology researchers use ImageJ on a daily basis, and exchange knowledge via its dedicated mailing list. Uses of ImageJ range from data visualization and teaching to advanced image processing and statistical analysis. The software's extensibility continues to attract biologists at all career stages as well as computer scientists who wish to effectively implement specific image-processing algorithms. In this review, we use the ImageJ project as a case study of how open-source software fosters its suites of software tools, making multitudes of image-analysis technology easily accessible to the scientific community. We specifically explore what makes ImageJ so popular, how it impacts the life sciences, how it inspires other projects, and how it is self-influenced by coevolving projects within the ImageJ ecosystem.

/pdf/the-imagej-ecosystem-an-open-platform-for-biomedical-image-idz281tl0y.pdf

The ImageJ ecosystem: An open platform for biomedical image analysis

The Konstanz Information Miner is a modular environment, which enables easy visual assembly and interactive execution of a data pipeline. It is designed as a teaching, research and collaboration platform, which enables simple integration of new algorithms and tools as well as data manipulation or visualization methods in the form of new modules or nodes. In this paper we describe some of the design aspects of the underlying architecture and briefly sketch how new nodes can be incorporated.

KNIME: The Konstanz Information Miner.

/pdf/knime-the-konstanz-information-miner-1wgaa2mdv0.pdf

KNIME: The Konstanz Information Miner

The Konstanz Information Miner is a modular environment, which enables easy visual assembly and interactive execution of a data pipeline. It is designed as a teaching, research and collaboration platform, which enables simple integration of new algorithms and tools as well as data manipulation or visualization methods in the form of new modules or nodes. In this paper we describe some of the design aspects of the underlying architecture, briey sketch how new nodes can be incorporated, and highlight some of the new features of version 2.0.

/pdf/knime-the-konstanz-information-miner-version-2-0-and-beyond-sy3199s2pb.pdf

KNIME - the Konstanz information miner: version 2.0 and beyond

https://www.uni-konstanz.de/bioml/bioml2/publications/Papers2004/GaBe04_mixedFRappendix_ijar.pdf

Influence of fuzzy norms and other heuristics on ¿Mixed fuzzy rule formation¿

This paper presents an approach to visualizing and exploring high-dimensional rules in two-dimensional views. The proposed method uses multi-dimensional scaling to place the rule centers and subsequently extends the rules' regions to depict their overlap. This results not only in a visualization of the rules' distribution but also enables the relationship to their immediate neighbors to be judged. The proposed technique is illustrated and discussed on a number of well-known benchmark data sets.

/pdf/rule-visualization-based-on-multi-dimensional-scaling-53vruoujlo.pdf

Thomas R. Gabriel

Papers

KNIME: The Konstanz Information Miner.

KNIME: The Konstanz Information Miner

KNIME - the Konstanz information miner: version 2.0 and beyond

Influence of fuzzy norms and other heuristics on ¿Mixed fuzzy rule formation¿

Rule Visualization based on Multi-Dimensional Scaling