The Comet Toolbox: Multiverse analysis for neuroimaging

About the toolbox

Please refer to the documentation for detailed information about the toolbox and the current features. The following README will only provide a very brief overview.

[!NOTE] This package is under active development. Please check regularly for new releases. If you have questions, suggestions, find a bug, or would like to contribute, feel free to open an issue on GitHub or contact us via the email address listed in the pyproject.toml.

Installation and usage

As Comet contains a fair amount of dependencies, it should be installed in a dedicated Python environment (e.g. conda or another environment manager of your choice) to avoid version conflicts. Comet runs on all major operating systems (Linux, Windows, macOS), although development and testing are primarily conducted on Linux. If you encounter any issues, please let us know via the issue tracker.

conda create -n comet python==3.13
conda activate comet
pip install "comet-toolbox[gui]"

Alternatively, you can install only the core toolbox without the GUI dependencies (e.g., for a high performance cluster or on Google Colab):

pip install comet-toolbox

Usage of the toolbox is then possible through either the GUI (might take 1-2 minutes to open on the first start):

comet-gui

or through the scripting API:

from comet import connectivity, graph, multiverse

A comprehensive set of usage examples are provided in the documentation.

Code structure

/
├─ src/comet/         ← Parent directory
│  ├─ connectivity.py ← Functional connectivity module
│  ├─ graph.py        ← Graph analysis module
│  ├─ multiverse.py   ← Multiverse analysis module
│  ├─ gui.py          ← Graphical user interface
│  ├─ utils.py        ← Miscellaneous helper functions
│  ├─ cifti.py        ← CIFTI related functions
│  └─ bids.py         ← BIDS related functions (placeholder)
├─ docs/              ← Documentation
├─ tutorials/         ← Example jupyter notebooks
├─ tests/             ← Unit tests
├─ pyproject.toml     ← Packaging & dependencies
└─ README.md          ← Project overview

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={https://doi.org/10.1162/IMAG.a.1122}
}

Contributing

We warmly welcome contributions and suggestions for new features! Comet is an open and collaborative project, and your input helps make it better for the entire community. Please see CONTRIBUTING.md for how to report bugs, run the tests, and submit pull requests, and CODE_OF_CONDUCT.md for the community standards we ask everyone to follow.