BrainGlobe version 1 is here! Head over to the blog to find out more


Brainreg & brainglobe-segmentation (formerly brainreg-segment):

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,

3D cell detection:

Tyson, A. L., Rousseau, C. V., Niedworok, C. J., Keshavarzi, S., Tsitoura, C., Cossell, L., Strom, M., Margrie, T. W. (2021) “A deep learning algorithm for 3D cell detection in whole mouse brain image datasets” PLOS Computational Biology 17(5): e1009074.


Claudi, F., Tyson, A. L., Petrucco, L., Margrie, T.W., Portugues, R., Branco, T. (2021) “Visualizing anatomically registered data with Brainrender” eLife 2021;10:e65751

BrainGlobe Atlas API:

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

aMAP (brainreg predecessor)

Niedworok, C.J, Brown, A.P.Y, Jorge Cardoso, M., Osten, P., Ourselin, S., Modat, M., Margrie, T.W. (2016) “aMAP is a validated pipeline for registration and segmentation of high-resolution mouse brain data” Nature Communications 7, 1187.