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

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#

Tutorials#

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

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

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)!

Notes#

  • 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”.

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