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

Note

It is possible to detect cells in a whole brain image and register this data to an atlas entirely within a graphical user interface. If you have not used brainmapper before, we recommend you take a look at the analysing brainwide distribution of cells tutorial.

User Guide

• Data requirements
• Command line interface
• Visualisation
• Output files
• Debugging common error messages
• Retraining the pre-trained network

Note

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.

Tutorials

• Whole brain cell detection and registration with the brainmapper command line tool

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”.