To test out brainreg, we supply a small mouse brain dataset to get you started.
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
Open a terminal (Linux) or your command prompt (Windows)
Activate your conda environment
To run brainreg, you need to know:
Where your data is (in this case, it's the path to the
Where you want to save the output data (we'll just save it into a directory called
brainreg_outputin the same directory as the
The pixel sizes of your data in microns (see Image definition for details). In this case, our data is 40um per pixel in in the coronal plane and the spacing of the planes is 50um.
The orientation of your data. The software needs to know how you acquired your data (coronal, saggital etc.). For this cellfinder uses bg-space. Full details on how to enter your data orientation can be found here, but 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 (you can see which are available by running
brainglobe list. In this case, we want to use a mouse atlas (as that's what our data is), and we'll use the 50um version of the Allen Mouse Brain Atlas.
To run brainreg, we put this all together in a single command:
brainreg test_brain brainreg_output -v 50 40 40 --orientation psl --atlas allen_mouse_50um
Lots of stuff will get printed to the console as brainreg runs, and when it's done (it should only take a minute or so), you will see something like:
INFO - MainProcess cli.py:230 - Finished. Total time taken: 0:00:29.15
This means that the registration is complete.
To view your data, run
napari from the same terminal/command as you ran brianreg (or open a new one and activate your conda environment). You can then drag and drop the
brainreg_output directory into napari, and see the results.