If you find cellfinder useful, and use it in your research, please cite the code repository:

Adam L. Tyson, Charly V. Rousseau, Christian J. Niedworok and Troy W. Margrie (2020). cellfinder: automated 3D cell detection and registration of whole-brain images. doi:10.5281/zenodo.3665329


If you use the image registration parts of cellfinder, please cite the brainreg repository:

Adam L. Tyson, Charly V. Rousseau, and Troy W. Margrie (2020). brainreg: automated 3D brain registration with support for multiple species and atlases. 10.5281/zenodo.3991718

And please also cite the BrainGlobe Atlas API that provided the atlas:

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,

Don't forget to cite the developers of the atlas that you used (e.g. the Allen Brain Atlas)