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., Cossell, L., Strom, M. and Margrie, T. W. (2021) “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:

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

Please also cite aMAP (the original pipeline from which the registration software is based):

Niedworok, C.J., Brown, A.P.Y., Jorge Cardoso, M., Osten, P., Ourselin, S., Modat, M., and Margrie, T.W., (2016). AMAP is a validated pipeline for registration and segmentation of high-resolution mouse brain data. Nature Communications. 7, 1–9.

Lastly, if you can, please cite the BrainGlobe Atlas API that provided the atlas:

Claudi, F., Petrucco, L., Tyson, A. L., Branco, T., Margrie, T. W. and 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)