Publications

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, doi.org/10.1038/s41598-021-04676-9

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. doi.org/10.1371/journal.pcbi.1009074

Brainrender:

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 doi.org/10.7554/eLife.65751

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 doi.org/10.21105/joss.02668

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. doi.org/10.1038/ncomms11879