Citing Cabana

If you use Cabana in your research, please cite the software and its components appropriately. This acknowledgment helps support the continued development of these tools and gives credit to the researchers who developed them.

Cabana Citation

Lin, X., Kallady, T., & Magenau, A. (2023). Cabana: ColAgen FiBre ANAlyzer.
Garvan Institute of Medical Research. https://github.com/Garvan-Data-Science-Platform/Cabana

BibTeX format:

@software{lin_cabana_2023,
  author = {Lin, Xufeng and Kallady, Tim and Magenau, Astrid},
  title = {Cabana: {ColAgen} {FiBre} {ANAlyzer}},
  url = {https://github.com/Garvan-Data-Science-Platform/Cabana},
  year = {2023},
  publisher = {Garvan Institute of Medical Research}
}

Component Citations

Cabana relies on several key components and algorithms. Please consider citing these as well when appropriate:

Ridge Detection

Steger, C. (1998). An unbiased detector of curvilinear structures. IEEE Transactions on Pattern Analysis and Machine Intelligence, 20(2), 113-125.

BibTeX format:

@article{steger_unbiased_1998,
  title = {An unbiased detector of curvilinear structures},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  author = {Steger, C.},
  year = {1998},
  volume = {20},
  number = {2},
  pages = {113--125}
}

Orientation Analysis (OrientationJ)

Püspöki, Z., Storath, M., Sage, D., & Unser, M. (2016). Transforms and Operators for Directional Bioimage Analysis: A Survey. Advances in Anatomy, Embryology and Cell Biology, 219, 69-93.

BibTeX format:

@article{puspoki_transforms_2016,
  title = {Transforms and {Operators} for {Directional} {Bioimage} {Analysis}: {A} {Survey}},
  journal = {Advances in Anatomy, Embryology and Cell Biology},
  author = {Püspöki, Z. and Storath, M. and Sage, D. and Unser, M.},
  year = {2016},
  volume = {219},
  pages = {69--93}
}

AnaMorf

Barry, D.J., Williams, G.A., & Chan, C. (2015). Automated Analysis of Filamentous Microbial Morphology with AnaMorf. Biotechnology Progress, 31(3), 849-852.

BibTeX format:

@article{barry_automated_2015,
  title = {Automated {Analysis} of {Filamentous} {Microbial} {Morphology} with {AnaMorf}},
  journal = {Biotechnology Progress},
  author = {Barry, D.J. and Williams, G.A. and Chan, C.},
  year = {2015},
  volume = {31},
  number = {3},
  pages = {849--852}
}

Max Inscribed Circles (Gap Analysis)

Hildebrand, T., & Rüegsegger, P. (1997). A new method for the model-independent assessment of thickness in three-dimensional images. Journal of Microscopy, 185(1), 67-75.

BibTeX format:

@article{hildebrand_new_1997,
  title = {A new method for the model-independent assessment of thickness in three-dimensional images},
  journal = {Journal of Microscopy},
  author = {Hildebrand, T. and Rüegsegger, P.},
  year = {1997},
  volume = {185},
  number = {1},
  pages = {67--75}
}

Acknowledgments

When publishing results obtained using Cabana, it is also recommended to include the following acknowledgment in your publication:

“Image analysis was performed using Cabana (ColAgen FiBre ANAlyzer), developed at the Garvan Institute of Medical Research by Lin, Kallady, and Magenau.”

Funding and Support

If applicable, please also acknowledge the funding and support that made Cabana development possible:

“Development of Cabana was supported by the Garvan Institute of Medical Research and [funding sources if provided by the developers].”

Contact

For questions regarding citation or acknowledgment in publications, please contact:

Xufeng Lin (x.lin@garvan.org.au)
Astrid Magenau (a.magenau@garvan.org.au)