Citing ConfUSIus¶

If you use ConfUSIus in your research, please cite it using the following reference:

Le Meur-Diebolt, S., & Cybis Pereira, F. (2026). ConfUSIus (v0.2.0). Zenodo. https://doi.org/10.5281/zenodo.18611124

Or in BibTeX format:

@software{confusius,
  author    = {Le Meur-Diebolt, Samuel and Cybis Pereira, Felipe},
  title     = {ConfUSIus},
  year      = {2026},
  publisher = {Zenodo},
  version   = {v0.2.0},
  doi       = {10.5281/zenodo.18611124},
  url       = {https://doi.org/10.5281/zenodo.18611124}
}

Third-Party Libraries¶

ConfUSIus stands on the shoulders of giants. It is built on top of many excellent open-source projects, without which it could not exist. If you use the features listed below, please consider citing the corresponding projects to support these efforts.

BrainGlobe¶

The atlas module uses the BrainGlobe Atlas API to interface with neuroanatomical atlases. If you use the atlas features in your research, please also cite BrainGlobe:

Claudi, F., Petrucco, L., Tyson, A. L., Branco, T., Margrie, T. W., & Portugues, R. (2020). BrainGlobe Atlas API: a common interface for neuroanatomical atlases. Journal of Open Source Software, 5(54), 2668. https://doi.org/10.21105/joss.02668

Or in BibTeX format:

@article{brainglobe,
  author    = {Claudi, Federico and Petrucco, Luigi and Tyson, Adam L. and
               Branco, Tiago and Margrie, Troy W. and Portugues, Ruben},
  title     = {{BrainGlobe} {Atlas} {API}: a common interface for neuroanatomical atlases},
  journal   = {Journal of Open Source Software},
  year      = {2020},
  volume    = {5},
  number    = {54},
  pages     = {2668},
  doi       = {10.21105/joss.02668},
  url       = {https://doi.org/10.21105/joss.02668}
}

Napari¶

The ConfUSIus GUI is built on top of napari, a powerful multi-dimensional image viewer for Python. If you use the ConfUSIus GUI in your research, please also cite napari:

napari contributors (2019). napari: a multi-dimensional image viewer for Python. Zenodo. https://doi.org/10.5281/zenodo.3555620

Or in BibTeX format:

@software{napari,
  author    = {{napari contributors}},
  title     = {napari: a multi-dimensional image viewer for {Python}},
  year      = {2019},
  publisher = {Zenodo},
  doi       = {10.5281/zenodo.3555620},
  url       = {https://doi.org/10.5281/zenodo.3555620}
}

Nilearn¶

The signal, glm, and connectivity modules contain code derived from Nilearn. If you use these modules in your research, please also cite Nilearn:

Nilearn contributors (2023). Nilearn. Zenodo. https://doi.org/10.5281/zenodo.8397156

Or in BibTeX format:

@software{nilearn,
  author    = {{Nilearn contributors}},
  title     = {Nilearn},
  year      = {2023},
  publisher = {Zenodo},
  doi       = {10.5281/zenodo.8397156},
  url       = {https://doi.org/10.5281/zenodo.8397156}
}

SimpleITK¶

The registration module uses SimpleITK for image registration and resampling. If you use the registration features in your research, please also cite SimpleITK:

Beare, R., Lowekamp, B., & Yaniv, Z. (2018). Image Segmentation, Registration and Characterization in R with SimpleITK. Journal of Statistical Software, 86(8), 1–35. https://doi.org/10.18637/jss.v086.i08

Or in BibTeX format:

@article{simpleitk,
  author  = {Beare, Richard and Lowekamp, Bradley and Yaniv, Ziv},
  title   = {Image Segmentation, Registration and Characterization in {R} with {SimpleITK}},
  journal = {Journal of Statistical Software},
  year    = {2018},
  volume  = {86},
  number  = {8},
  pages   = {1--35},
  doi     = {10.18637/jss.v086.i08},
  url     = {https://doi.org/10.18637/jss.v086.i08}
}

Templates¶

Pepe, Mariani et al. (2026)¶

The fetch_template_pepe_mariani_2026 function provides a mouse fUSI template derived from Pepe, Mariani et al. (2026). If you use this template in your research, please also cite the corresponding article:

Pepe, C., Mariani, J.-C., Urosevic, M., Gini, S., Stuefer, A., Ricci, F., Galbusera, A., Iurilli, G., & Gozzi, A. (2026). Structural and dynamic embedding of the mouse functional connectome revealed by functional ultrasound imaging (fUSI). bioRxiv. https://doi.org/10.64898/2026.02.05.704055

Or in BibTeX format:

@article{pepe2026fusi,
  author    = {Pepe, Chiara and Mariani, Jean-Charles and Urosevic, Mila and Gini, Silvia and
               Stuefer, Alexia and Ricci, Fabio and Galbusera, Alberto and Iurilli, Giuliano and
               Gozzi, Alessandro},
  title     = {Structural and dynamic embedding of the mouse functional connectome revealed by
               functional ultrasound imaging ({fUSI})},
  journal   = {bioRxiv},
  year      = {2026},
  publisher = {Cold Spring Harbor Laboratory},
  doi       = {10.64898/2026.02.05.704055},
  url       = {https://doi.org/10.64898/2026.02.05.704055}
}