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

Abstract

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.

Analysis of Forest Fragmentation and Connectivity Using Fractal Dimension and Succolarity

“…Succolarity, potential succolarity, and ∆ succolarity were calculated using the succolarity plugin from the ComsystanJ (Complex Systems Analysis for ImageJ) [76] collection plugins version 1.1.2 of Fiji/ImageJ2 2.14.0/1.54h java 1.8.0_322 64-bit [77]. Succolarity is a binary algorithm that operates on a [0, >0] scale by flooding the black pixels of a binary image.…”

“…The FFI and FFDI were calculated using the fractal fragmentation indices plugin available in the ComsystanJ collection plugins [76] for Fiji/ImageJ2 2.14.0/1.54h [77]. These plugins provide binary algorithms that operate on a [0, >0] scale by analysing the white pixels of a binary image.…”

“…As highlighted by Loke and Chisholm (2022), this standardization applies to both algorithmically generated images and those derived from empirical data [81]. Secondly, the Image generator-Fractal HRM from ComsystanJ collection plugin [76] was used within the Fiji/ImageJ2 2.14.0/1.54h software to generate a hierarchically structured random map (HRM) image. The HRM image was created using a recursive algorithm inspired by the curdling and random trema generation method introduced by Plotnick [27,63].…”

“…These maps can simulate landscapes with varying levels of clustering, fragmentation, and connectivity, achieved through the processes of curdling and random trema. It is important to note that two surfaces may share the same overall fill space and yet diverge in their degree of curdling, which denotes Secondly, the Image generator-Fractal HRM from ComsystanJ collection plugin [76] was used within the Fiji/ImageJ2 2.14.0/1.54h software to generate a hierarchically structured random map (HRM) image. The HRM image was created using a recursive algorithm inspired by the curdling and random trema generation method introduced by Plotnick [27,63].…”

Fractal complexity of Escherichia coli nutrient transport channels is influenced by cell shape and growth environment

“…Fractal complexity quantification Fractal complexity was quantified using the FIJI plugin ComsystanJ (Complex Systems Analysis for ImageJ) [34], version 1.0.0 (https://github.com/comsystan/comsystanj). The "2D image" version of the plugin was used on the images, all of which had a size of 2048 x 2048 pixels.…”