ImageJ2: ImageJ for the next generation of scientific image data

ImageJ2: ImageJ for the next generation of scientific image data

3 Nov 2017 | Curtis T Rueden, Johannes Schindelin, Mark C Hiner, Barry E DeZonia, Alison E Walter, Ellen T Arena, Kevin W Eliceiri
ImageJ2 is a next-generation version of ImageJ, designed to meet the evolving needs of scientific image analysis. It was developed to address the limitations of the original ImageJ 1.x, which had a growing user base, diverging plugin suites, and technical constraints. ImageJ2 provides a more powerful and flexible platform, with a redesigned plugin mechanism that allows for extensibility at every level. It separates concerns, fully decoupling the data model from the user interface, and emphasizes integration with external applications to maximize interoperability. The new data model supports arbitrarily large, N-dimensional datasets, which are increasingly common in modern image acquisition. Backwards compatibility is maintained, allowing users and developers to migrate to these new methods at their own pace. The development of ImageJ2 was driven by several key motivations: supporting the next generation of image data, enabling new software collaborations, and broadening the ImageJ community. ImageJ2 is designed to be a modular, multi-layered set of functions with each layer encapsulated and building upon lower layers. It provides robust support for N-dimensional image data and includes built-in routines for standard tasks in image processing and analysis. The plugin framework allows for easy extension by the community, with a focus on interoperability and open standards for data storage and exchange. ImageJ2 is built on the SciJava framework, which provides a set of standard Java libraries for managing extensible applications. It includes the ImgLib2 container model for general image analysis, the SCIFIO library for reading, writing, and translating image formats, and the ImageJ component for low-level image processing. These layers form the ImageJ software stack, the core set of components upon which ImageJ-based applications are built. The SciJava Common library provides the core framework for creating extensible applications, including services for plugin management, event handling, logging, object management, thread management, and input/output operations. The plugin framework allows for the definition of plugins that add new features or modify existing behavior, with a focus on extensibility and interoperability. The module framework enables ImageJ algorithms to be decoupled from user interfaces and applications, allowing for seamless integration with other scientific software. The ImageJ Ops component provides a shared, extensible library of reusable image processing operations, covering a wide range of functionalities such as image arithmetic, trigonometry, Fourier transformations, deconvolution, and more. It is designed to be easy to use and extend, powerful and general, and high performance. The Ops framework uses a plugin-based design to enable "extensible case logic," allowing for efficient chaining of operations and special ops for type-safe and efficient chaining. The Ops library also supports GPU and cluster-based implementations, enabling automatic selection based on the currently available hardware environment.ImageJ2 is a next-generation version of ImageJ, designed to meet the evolving needs of scientific image analysis. It was developed to address the limitations of the original ImageJ 1.x, which had a growing user base, diverging plugin suites, and technical constraints. ImageJ2 provides a more powerful and flexible platform, with a redesigned plugin mechanism that allows for extensibility at every level. It separates concerns, fully decoupling the data model from the user interface, and emphasizes integration with external applications to maximize interoperability. The new data model supports arbitrarily large, N-dimensional datasets, which are increasingly common in modern image acquisition. Backwards compatibility is maintained, allowing users and developers to migrate to these new methods at their own pace. The development of ImageJ2 was driven by several key motivations: supporting the next generation of image data, enabling new software collaborations, and broadening the ImageJ community. ImageJ2 is designed to be a modular, multi-layered set of functions with each layer encapsulated and building upon lower layers. It provides robust support for N-dimensional image data and includes built-in routines for standard tasks in image processing and analysis. The plugin framework allows for easy extension by the community, with a focus on interoperability and open standards for data storage and exchange. ImageJ2 is built on the SciJava framework, which provides a set of standard Java libraries for managing extensible applications. It includes the ImgLib2 container model for general image analysis, the SCIFIO library for reading, writing, and translating image formats, and the ImageJ component for low-level image processing. These layers form the ImageJ software stack, the core set of components upon which ImageJ-based applications are built. The SciJava Common library provides the core framework for creating extensible applications, including services for plugin management, event handling, logging, object management, thread management, and input/output operations. The plugin framework allows for the definition of plugins that add new features or modify existing behavior, with a focus on extensibility and interoperability. The module framework enables ImageJ algorithms to be decoupled from user interfaces and applications, allowing for seamless integration with other scientific software. The ImageJ Ops component provides a shared, extensible library of reusable image processing operations, covering a wide range of functionalities such as image arithmetic, trigonometry, Fourier transformations, deconvolution, and more. It is designed to be easy to use and extend, powerful and general, and high performance. The Ops framework uses a plugin-based design to enable "extensible case logic," allowing for efficient chaining of operations and special ops for type-safe and efficient chaining. The Ops library also supports GPU and cluster-based implementations, enabling automatic selection based on the currently available hardware environment.
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