Citing cellfinder

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, doi.org/10.1101/2020.10.21.348771

registration

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. https://doi.org/10.1038/ncomms11879

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, https://doi.org/10.21105/joss.02668

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