brainmapper command line tool#

brainmapper can:

  • Detect labelled cells in 3D in whole-brain images (many hundreds of GB)

  • Register the image to an atlas (such as the Allen Mouse Brain Atlas)

  • Segment the brain based on the reference atlas

  • Calculate the volume of each brain area, and the number of labelled cells within it

  • Transform everything into standard space for analysis and visualisation

User Guide#


If you would like to use brainmapper offline, you will need to download an appropriate atlas and download a pre-trained cellfinder model in advance.


Citing cellfinder#

If you find brainmapper useful, and use it in your research, please cite the papers outlining the registration and cell detection algorithms:

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, 12, 867

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

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)!


  • As of version 1.0.0 of brainglobe-workflows, the Docker image for brainmapper has been discontinued.

  • Prior to the release of cellfinder v1.0.0, this workflow and command-line tool was called “cellfinder”.