Registering a whole-brain dataset to the Allen Mouse Brain atlas with brainreg#


For full information on how to use brainreg, please see the brainreg page

Setting up#

To test out brainreg, we supply a small mouse brain dataset to get you started. To begin:

  • Download the data from here (the dataset is ~10MB, so it should download quickly).

  • Unzip the data to a directory of your choice (doesn’t matter where). You should end up with a directory called test_brain with 270 .tif images

To run brainreg, you need to know:

  • Where your data is (in this case, it’s the path to the test_brain directory)

  • Where you want to save the output data (we’ll just save it into a directory called brainreg_outputin the same directory as the test_brain)

  • The pixel sizes of your data in microns (see Image definition for details). In this case, our data is 40μm per pixel in the coronal plane, and the spacing of the planes is 50μm.

  • The orientation of your data. The software needs to know how you acquired your data (coronal, sagittal etc.). For this BrainGlobe uses bg-space. For this tutorial, the orientation is psl, which means that the data origin is the most posterior, superior, left voxel. For more details see Image definition

  • Which atlas you want to use (the list of available atlases is available here). In this case, we want to use a mouse atlas (as that’s what our data is), and we’ll use the 50μm version of the Allen Mouse Brain Atlas


In this tutorial we will use the 50μm version of the Allen Mouse Brain Atlas. Low-resolution atlases like this are usually only used for testing (the registration will work much quicker at lower resolution). In this case, the test input data is very low resolution, so using a higher resolution atlas doesn’t make much sense.

When using your own data, you’ll probably find that higher resolution atlases provide better results. Make sure to test out the different resolutions to see what works best.

Running the registration#

There are two ways to run the registration using brainreg. If you’re just getting started, we recommend the napari plugin. This provides a graphical user interface, and makes it easier to tweak parameters.

If you need to run brainreg on many samples, or on a remote machine (e.g., using an institutional high-performance computing system), there is a command-line interface.

Whichever interface you use, the results will be identical.


The results are likely not perfect because (for speed and simplicity) we:

  • Used very low-resolution data

  • Use a low-resolution atlas

  • Left all the parameters as default (which were optimised for higher resolution atlases)