Comet - A toolbox for dynamic functional connectivity and multiverse analysis

Yet another toolbox?

You might ask yourself, “Why do I need yet another toolbox for dynamic functional connectivity (dFC) analysis and network neuroscience?” The answer is simple: the reproducibility crisis, driven in part by the maze of arbitrary yet defensible decisions in our analyses.

To address this, we introduce the Comet Toolbox: A tool that helps ensure your findings don’t get lost in the Bermuda Triangle of irreproducible results. Whether you want to take full advantage of multiverse analysis or stick with traditional analyses, Comet lets you explore a broad range of methodological decisions, making your research more robust and transparent.

From dFC estimation to graph analyses, Comet offers a wide range of methods. Plus, with an easy-to-use graphical user interface and comprehensive demo scripts, even the most Python-phobic among us can dive in and start exploring brain dynamics like never before. So, buckle up, and let’s bring some cosmic clarity to your research universe!

Note

The Toolbox is under active development. If you have any questions, suggestions, or want to contribute, please do not hesitate to reach out via GitHub or email.

Current features

Functional Connectivity	Graph Analysis	Multiverse Analysis
Continuous Sliding Window Jackknife Correlation Flexible Least Squares Spatial Distance Temporal Derivatives Dynamic Conditional Correlation Phase Synchronization Leading Eigenvector Dynamics Wavelet Coherence Edge-centric connectivity State-Based SW Clustering Co-activation Patterns Discrete HMM Continuous HMM K-SVD K-means clustering for all continuous measures Static Pearson Correlation Partial Correlation Mutual Information	Optimized implementations Average Path Length Global Efficiency Nodal Efficiency Small-World Sigma Small-World Propensity Matching Index Standard Graph Functions Threshold Binarise Symmetrise Handle negative weights ... BCT Integration All BCT functions can be used seamlessly for multiverse analysis Many BCT functions are available in the GUI	Simple Definition Forking paths as dictionary Analysis pipeline template with decision points Generation Universes are created as individual scripts Modular approach Complex multiverse structures Analysis Individual universes Entire multiverse (parallel) Visualization Multiverse summary Multiverse as a network Specification Curve analysis

Citing

If you use Comet in your work, please cite the following paper:

Burkhardt, M., & Gießing, C. (2026). The Comet Toolbox: Improving Robustness in Network Neuroscience Through Multiverse Analysis. Imaging Neuroscience. https://doi.org/10.1162/IMAG.a.1122

@article{Burkhardt2026,
  title   = {The Comet Toolbox: Improving Robustness in Network Neuroscience Through Multiverse Analysis},
  author  = {Burkhardt, Micha and Giessing, Carsten},
  journal = {Imaging Neuroscience},
  year    = {2026},
  doi     = {10.1162/IMAG.a.1122}
}