About ComsystanJ
ComsystanJ (Complex Systems Analysis for ImageJ) is a collection of ImageJ2/Fiji plugins to compute the complexity, fractal dimension and other nonlinear measures of 1D signals, 2D images and 3D image volumes. It is recommended to use it with Fiji. Developed and maintained by Helmut Ahammer.
List of features
1D signals
- Signal opener, Signal generator
Preprocessing
- Cut out, Filter, Mathematics, Noise, Resampling, Surrogates
Detection
- Event detection, QRS peak detection (from file)
Linear analyses
- Autocorrelation, FFT, Statistics
Complexity analyses
- Allometric scaling, Detrended fluctuation analysis, Generalised DFA, Kolmogorov complexity and Logical depth, Lyapunov exponent, Poincare plot, Porta Guzik Ehler indices, Recurrence quantification analysis, Standard HRV measurements, Symbolic aggregation
Entropy analyses
- Generalised entropies, Permutation entropy, Sample entropy
Fractal analyses
- Fragmentation dimension, Higuchi dimension, Hurst coefficient (HK, RS, SP), Hurst coefficient (PSD), Katz dimension, Petrosian dimension, RSE dimension (Roughness dimension), Sevcik dimension, Tug of war dimension, Walking divider dimension
2D images
- Image opener, Image generator
Preprocessing
- Auto crop borders, Filter, Histogram modification, Noise, Particles to stack, Segmentation - RGB relative, Surrogates
Complexity analyses
- Kolmogorov complexity and Logical depth
Entropy analyses
- Generalised entropies
Fractal analyses
- Box counting dimension, Correlation dimension, Fractal correlation dimension, Directional correlation dimension, FFT dimension, Link to FracLac, Fractal fragmentation indices, Generalised dimensions, Higuchi dimension 1D, Higuchi dimension 2D, Lacunarity, Mass radius dimension, Minkowski dimension, Perimeter area dimension, Pyramid dimension, Succolarity, Tug of war dimension, Walking divider dimension
3D Image volume
- Image volume opener, Image volume generator
3D Preprocessing
- 3D Filter, 3D Noise, 3D Surrogates
3D Complexity analyses
- 3D Kolmogorov complexity and Logical depth
3D Entropy analyses
- 3D Generalised entropies
3D Fractal analyses
- 3D Box counting Dimension, 3D Correlation dimension, 3D FFT dimension, 3D Fractal fragmentation indices, 3D Generalised dimensions, 3D Higuchi dimension, 3D Lacunarity, 3D Minkowski dimension, 3D Succolarity, 3D Tug of war dimension
Downloads
You can download ComsystanJ here
Installation
Copy the ComsystanJ-x.x.x.jar file to the Fiji’s plugins folder. Delete the old ComsystanJ jar file if it exists.
Homepage and description
Citing ComsystanJ
If you use ComsystanJ plugins and publish your work, please cite following publication:
Helmut Ahammer, Martin A. Reiss, Moritz Hackhofer, Ion Andronache, Marko Radulovic, Fabián Labra-Spröhnle, and Herbert Franz Jelinek. „ComsystanJ: A Collection of Fiji/ImageJ2 Plugins for Nonlinear and Complexity Analysis in 1D, 2D and 3D“. PLOS ONE 18, Nr. 10, 2023, e0292217, https://doi.org/10.1371/journal.pone.0292217
Contact
Helmut Ahammer e-mail comsystan@outlook.com
