citation.md

# 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’ PLOS Computational Biology, 17(5), e1009074 [https://doi.org/10.1371/journal.pcbi.1009074](https://doi.org/10.1371/journal.pcbi.1009074) ## registration If you use the image registration parts of cellfinder, please cite [brainreg](https://github.com/brainglobe/brainreg): > Tyson, A. L., Vélez-Fort, M., Rousseau, C. V., Cossell, L., Tsitoura, C., Lenzi, S. C., Obenhaus, H. A., Claudi, F., Branco, T., Margrie, T. W. (2022) “Accurate determination of marker location within whole-brain microscopy images’ Scientific Reports. [https://doi.org/10.1038/s41598-021-04676-9](https://doi.org/10.1038/s41598-021-04676-9) 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](https://doi.org/10.1038/ncomms11879) Lastly, if you can, please cite the [BrainGlobe Atlas API](https://github.com/brainglobe/bg-atlasapi) 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](https://doi.org/10.21105/joss.02668) {% hint style="info" %} Don't forget to cite the developers of the atlas that you used (e.g. the Allen Brain Atlas) {% endhint %}