ComsystanJ: A collection of Fiji/ImageJ2 plugins for nonlinear and complexity analysis in 1D, 2D and 3D.

Complex systems such as the global climate, biological organisms, civilisation, technical or social networks exhibit diverse behaviours at various temporal and spatial scales, often characterized by nonlinearity, feedback loops, and emergence. These systems can be characterized by physical quantities such as entropy, information, chaoticity or fractality rather than classical quantities such as time, velocity, energy or temperature. The drawback of these complexity quantities is that their definitions are not always mathematically exact and computational algorithms provide estimates rather than exact values. Typically, evaluations can be cumbersome, necessitating specialized tools. We are therefore introducing ComsystanJ, a novel and user-friendly software suite, providing a comprehensive set of plugins for complex systems analysis, without the need for prior programming knowledge. It is platform independent, end-user friendly and extensible. ComsystanJ combines already known algorithms and newer methods for generalizable analysis of 1D signals, 2D images and 3D volume data including the generation of data sets such as signals and images for testing purposes. It is based on the framework of the open-source image processing software Fiji and ImageJ2. ComsystanJ plugins are macro recordable and are maintained as open-source software. ComsystanJ includes effective surrogate analysis in all dimensions to validate the features calculated by the different algorithms. Future enhancements of the project will include the implementation of parallel computing for image stacks and volumes and the integration of artificial intelligence methods to improve feature recognition and parameter calculation.