Citing cellfinder


If you find cellfinder useful, and use it in your research, please cite the preprint outlining the cell detection algorithm:

Tyson, A. L., Rousseau, C. V., Niedworok, C. J., Keshavarzi, S., Tsitoura, C. and Margrie, T. W. (2020) “A deep learning algorithm for 3D cell detection in whole mouse brain image datasets’ bioRxiv,


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)